Correlation between copy number variation genes (focal events) and molecular subtypes

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 101 focal events and 12 molecular subtypes across 539 patients, 1081 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p35.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q13 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p24.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8p11.22 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_8p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_11p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q24.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q32.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p13 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p36.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q11 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q22.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.43 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 101 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 1081 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1p35 2	56 (10%)	483	0.0426 (0.0481)	0.00054 (0.000742)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00015 (0.000219)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00807 (0.00978)	0.00029 (0.000409)
amp 1p34 2	73 (14%)	466	0.0108 (0.0129)	0.00124 (0.00164)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0031 (0.00395)	2e-05 (3.22e-05)
amp 1q21 3	243 (45%)	296	0.0258 (0.0297)	0.00538 (0.00665)	1e-05 (1.71e-05)	0.00683 (0.00837)	0.0137 (0.0161)	0.0205 (0.0238)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	4e-05 (6.19e-05)	0.00013 (0.00019)	9e-05 (0.000134)
amp 1q22	256 (47%)	283	0.0472 (0.0531)	0.0108 (0.0129)	1e-05 (1.71e-05)	0.00197 (0.00257)	0.0276 (0.0317)	0.0189 (0.022)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00202 (0.00263)	0.00052 (0.000717)
amp 3q26 2	175 (32%)	364	6e-05 (9.1e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 3q26 2	164 (30%)	375	0.00045 (0.000626)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 4p16 3	52 (10%)	487	0.0426 (0.0481)	0.00751 (0.00918)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00016 (0.000233)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00616 (0.00758)	0.00109 (0.00145)
amp 6p24 2	117 (22%)	422	0.00471 (0.00589)	0.00058 (0.000792)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)
amp 8p11 21	162 (30%)	377	0.0169 (0.0197)	0.0296 (0.0338)	1e-05 (1.71e-05)	0.0118 (0.0139)	0.00155 (0.00203)	6e-05 (9.1e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	0.00111 (0.00147)	0.00385 (0.00486)
amp 8q24 21	215 (40%)	324	0.00426 (0.00535)	0.00611 (0.00753)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)
amp 11p11 2	52 (10%)	487	0.00266 (0.0034)	0.00796 (0.00969)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00153 (0.00201)	0.00906 (0.0109)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0273 (0.0313)	0.0196 (0.0228)
amp 16p11 2	66 (12%)	473	0.0084 (0.0102)	0.00513 (0.00638)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00238 (0.00307)	0.00027 (0.000381)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00081 (0.00109)	0.00303 (0.00387)
amp 17q25 1	105 (19%)	434	5e-05 (7.66e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 19p13 2	92 (17%)	447	4e-05 (6.19e-05)	4e-05 (6.19e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	0.00664 (0.00815)
amp 19p13 12	99 (18%)	440	0.00358 (0.00454)	0.00017 (0.000246)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	7e-05 (0.000106)
amp 19q12	121 (22%)	418	0.00666 (0.00817)	7e-05 (0.000106)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)
amp 20q11 21	152 (28%)	387	0.00094 (0.00126)	4e-05 (6.19e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	0.00013 (0.00019)
amp 20q13 12	152 (28%)	387	0.0112 (0.0133)	0.00939 (0.0113)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	8e-05 (0.00012)	1e-05 (1.71e-05)
amp 20q13 33	153 (28%)	386	0.0111 (0.0132)	0.0014 (0.00184)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00023 (0.000326)	1e-05 (1.71e-05)
del 1p36 21	71 (13%)	468	0.0328 (0.0374)	0.0017 (0.00223)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00351 (0.00446)	0.00062 (0.000842)
del 1p36 11	83 (15%)	456	0.0422 (0.0478)	0.00775 (0.00947)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00052 (0.000717)	2e-05 (3.22e-05)
del 2q22 1	49 (9%)	490	0.00799 (0.0097)	0.00518 (0.00643)	1e-05 (1.71e-05)	5e-05 (7.66e-05)	2e-05 (3.22e-05)	0.00065 (0.00088)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00026 (0.000368)	0.00502 (0.00625)
del 3p14 2	79 (15%)	460	0.0426 (0.0481)	0.00798 (0.0097)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00532 (0.00659)	1e-05 (1.71e-05)
del 4p16 3	94 (17%)	445	0.0113 (0.0133)	0.00108 (0.00144)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	6e-05 (9.1e-05)	7e-05 (0.000106)
del 4p15 31	99 (18%)	440	0.0113 (0.0133)	0.0096 (0.0115)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 4q22 1	106 (20%)	433	0.00369 (0.00467)	0.00011 (0.000163)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)
del 4q34 3	130 (24%)	409	0.00402 (0.00506)	0.00018 (0.00026)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 5q12 1	111 (21%)	428	0.0116 (0.0137)	0.00984 (0.0118)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 7p22 3	72 (13%)	467	0.00051 (0.000706)	0.01 (0.012)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00094 (0.00126)	2e-05 (3.22e-05)
del 8p23 2	119 (22%)	420	0.00218 (0.00283)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 8p21 2	117 (22%)	422	0.00258 (0.0033)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 9q21 2	129 (24%)	410	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	9e-05 (0.000134)
del 9q34 2	132 (24%)	407	4e-05 (6.19e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00017 (0.000246)	4e-05 (6.19e-05)
del 14q13 1	73 (14%)	466	0.00858 (0.0104)	0.0052 (0.00645)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00067 (0.000906)	0.0002 (0.000287)
del 15q15 1	140 (26%)	399	0.0432 (0.0488)	0.0108 (0.0129)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 15q23	115 (21%)	424	0.00255 (0.00327)	0.00052 (0.000717)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 16p13 3	92 (17%)	447	0.011 (0.0131)	0.00968 (0.0116)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)
del 16q21	154 (29%)	385	0.00104 (0.00139)	8e-05 (0.00012)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	1e-05 (1.71e-05)
del 16q23 1	166 (31%)	373	0.00484 (0.00604)	0.00019 (0.000274)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)
del 17p13 3	122 (23%)	417	0.00072 (0.00097)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00121 (0.0016)
del 17p11 2	128 (24%)	411	0.00087 (0.00117)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	0.00012 (0.000177)
del 17q11 2	105 (19%)	434	0.00053 (0.000729)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00231 (0.00299)	0.0274 (0.0314)
del 17q21 31	114 (21%)	425	6e-05 (9.1e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00021 (3e-04)	0.0154 (0.018)
del 19p13 3	157 (29%)	382	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 19q13 43	67 (12%)	472	0.00089 (0.00119)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00358 (0.00454)	2e-05 (3.22e-05)
del 22q13 32	140 (26%)	399	6e-05 (9.1e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	8e-05 (0.00012)	1e-05 (1.71e-05)
del xp21 1	88 (16%)	451	0.00053 (0.000729)	0.00106 (0.00141)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	4e-05 (6.19e-05)	2e-05 (3.22e-05)
amp 2q13	119 (22%)	420	0.211 (0.223)	0.0292 (0.0334)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 5p15 33	89 (17%)	450	0.292 (0.306)	0.044 (0.0497)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 8q24 21	209 (39%)	330	0.0237 (0.0274)	0.0723 (0.0799)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 11q13 2	74 (14%)	465	0.00058 (0.000792)	0.00943 (0.0113)	1e-05 (1.71e-05)	0.00016 (0.000233)	0.00198 (0.00258)	0.0007 (0.000944)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	0.071 (0.0787)	0.00437 (0.00548)
amp 14q24 3	64 (12%)	475	0.0717 (0.0794)	0.01 (0.012)	1e-05 (1.71e-05)	5e-05 (7.66e-05)	0.00173 (0.00226)	0.0116 (0.0137)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0466 (0.0524)	0.0154 (0.0181)
amp 17q12	75 (14%)	464	0.11 (0.12)	0.00225 (0.00292)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00024 (0.00034)	1e-05 (1.71e-05)
amp 20p13	117 (22%)	422	0.122 (0.132)	0.05 (0.0561)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	9e-05 (0.000134)	5e-05 (7.66e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.003 (0.00383)	5e-05 (7.66e-05)
del 6q26	46 (9%)	493	0.35 (0.366)	0.0302 (0.0345)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00037 (0.000519)	0.00149 (0.00196)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0002 (0.000287)	0.00021 (3e-04)
del 9p23	80 (15%)	459	0.122 (0.132)	0.0498 (0.0559)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00033 (0.000464)	0.00056 (0.000768)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00403 (0.00507)	0.0112 (0.0133)
del 13q11	98 (18%)	441	0.41 (0.426)	0.0395 (0.0448)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00452 (0.00567)	0.00661 (0.00812)
del 16q22 3	158 (29%)	381	0.0516 (0.0578)	0.0102 (0.0122)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	8e-05 (0.00012)	1e-05 (1.71e-05)
del 22q12 1	95 (18%)	444	0.00252 (0.00324)	0.00738 (0.00903)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00058 (0.000792)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	0.00794 (0.00967)	0.0998 (0.109)
amp 2p24 3	122 (23%)	417	0.359 (0.374)	0.133 (0.143)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	4e-05 (6.19e-05)	0.0001 (0.000149)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	5e-05 (7.66e-05)	0.00041 (0.000573)
amp 3p25 1	82 (15%)	457	0.272 (0.285)	0.0532 (0.0594)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00065 (0.00088)	4e-05 (6.19e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00329 (0.00419)	0.00454 (0.00568)
amp 6q25 1	88 (16%)	451	0.464 (0.48)	1 (1.00)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00375 (0.00474)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	0.011 (0.0131)	0.0176 (0.0205)
amp 9p24 2	65 (12%)	474	0.168 (0.179)	0.0875 (0.0961)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0004 (0.00056)	0.00023 (0.000326)
amp 9q34 3	39 (7%)	500	0.159 (0.17)	0.0135 (0.0159)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0105 (0.0125)	0.00205 (0.00267)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	8e-05 (0.00012)	1e-05 (1.71e-05)	0.0732 (0.0808)	0.00785 (0.00958)
amp 11q14 1	60 (11%)	479	0.124 (0.134)	0.112 (0.122)	1e-05 (1.71e-05)	6e-05 (9.1e-05)	0.0253 (0.0292)	0.00224 (0.00291)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	0.0289 (0.0331)	0.0263 (0.0303)
amp 12q13 11	87 (16%)	452	0.639 (0.655)	0.203 (0.215)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	5e-05 (7.66e-05)	0.00062 (0.000842)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00249 (0.0032)	7e-05 (0.000106)
amp 12q13 2	100 (19%)	439	0.356 (0.371)	0.0875 (0.0961)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00011 (0.000163)	0.00055 (0.000755)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0002 (0.000287)	0.00021 (3e-04)
amp 13q34	58 (11%)	481	0.846 (0.863)	0.165 (0.177)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00062 (0.000842)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00019 (0.000274)	4e-05 (6.19e-05)
amp 14q32 33	79 (15%)	460	0.503 (0.519)	0.314 (0.328)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00022 (0.000313)	0.00047 (0.000653)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00499 (0.00622)	0.0318 (0.0363)
amp 17q11 2	71 (13%)	468	0.121 (0.131)	0.0511 (0.0572)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	6e-05 (9.1e-05)	1e-05 (1.71e-05)
amp 18p11 31	96 (18%)	443	0.212 (0.223)	0.0556 (0.0621)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)
amp 18q11 2	69 (13%)	470	0.109 (0.119)	0.184 (0.196)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
amp 22q12 2	62 (12%)	477	0.353 (0.368)	0.194 (0.206)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 7q11 22	41 (8%)	498			1e-05 (1.71e-05)	2e-05 (3.22e-05)	0.00064 (0.000869)	0.00248 (0.00319)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0111 (0.0131)	0.0046 (0.00575)
del 7q31 1	55 (10%)	484	0.135 (0.145)	0.166 (0.177)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	4e-05 (6.19e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00015 (0.000219)	0.00015 (0.000219)
del 7q36 1	63 (12%)	476	0.411 (0.426)	0.0793 (0.0874)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00013 (0.00019)	3e-05 (4.73e-05)
del 10q21 1	50 (9%)	489			1e-05 (1.71e-05)	1e-05 (1.71e-05)	7e-05 (0.000106)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)
del 10q23 31	78 (14%)	461	0.133 (0.143)	0.166 (0.177)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00013 (0.00019)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	8e-05 (0.00012)	4e-05 (6.19e-05)
del 11p15 5	104 (19%)	435	0.352 (0.367)	0.195 (0.206)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 11q14 1	69 (13%)	470			1e-05 (1.71e-05)	1e-05 (1.71e-05)	5e-05 (7.66e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00011 (0.000163)	1e-05 (1.71e-05)
del 11q25	94 (17%)	445	0.135 (0.145)	0.168 (0.179)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00028 (0.000395)	1e-05 (1.71e-05)
del 12q23 1	56 (10%)	483			1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	2e-05 (3.22e-05)
del 12q24 33	66 (12%)	473			1e-05 (1.71e-05)	1e-05 (1.71e-05)	9e-05 (0.000134)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)
del 13q14 2	106 (20%)	433	1 (1.00)	0.193 (0.205)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	4e-05 (6.19e-05)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0224 (0.0258)	0.0166 (0.0194)
del 18q21 2	90 (17%)	449	0.624 (0.641)	0.251 (0.264)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00043 (6e-04)	0.00142 (0.00187)
del 18q23	98 (18%)	441	0.621 (0.638)	0.254 (0.267)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00013 (0.00019)	0.00173 (0.00226)
del 19p12	58 (11%)	481			1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0012 (0.00159)	3e-05 (4.73e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00586 (0.00723)	0.0002 (0.000287)
amp 5q35 3	57 (11%)	482	0.135 (0.145)	0.169 (0.179)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	0.00035 (0.000492)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0699 (0.0775)	0.0007 (0.000944)
amp 12p12 1	92 (17%)	447	0.526 (0.542)	0.538 (0.554)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0882 (0.0967)	0.00097 (0.00129)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.0007 (0.000944)	6e-05 (9.1e-05)
amp 1q42 3	227 (42%)	312	0.0799 (0.088)	0.0385 (0.0438)	1e-05 (1.71e-05)	0.0724 (0.0799)	0.0625 (0.0695)	0.0313 (0.0357)	0.0196 (0.0228)	0.00059 (0.000804)	0.00031 (0.000436)	0.0334 (0.038)	0.391 (0.406)	0.0131 (0.0154)
amp 3p14 1	65 (12%)	474	0.76 (0.777)	0.513 (0.529)	1e-05 (1.71e-05)	0.00024 (0.00034)	0.113 (0.123)	0.0192 (0.0224)	1e-05 (1.71e-05)	2e-05 (3.22e-05)	0.00013 (0.00019)	0.00044 (0.000614)	0.0138 (0.0161)	0.0616 (0.0685)
amp 7q31 2	93 (17%)	446	0.638 (0.654)	0.434 (0.45)	1e-05 (1.71e-05)	0.0004 (0.00056)	0.133 (0.143)	0.00127 (0.00168)	0.00096 (0.00128)	0.00012 (0.000177)	0.00052 (0.000717)	0.0048 (0.00599)	0.00229 (0.00297)	0.0897 (0.0983)
amp xp11 23	90 (17%)	449	0.433 (0.449)	0.814 (0.832)	1e-05 (1.71e-05)	0.0013 (0.00171)	0.526 (0.542)	0.0922 (0.101)	3e-05 (4.73e-05)	0.00045 (0.000626)	0.00609 (0.00751)	0.0005 (0.000693)	0.00236 (0.00305)	0.00787 (0.0096)
amp xq28	93 (17%)	446	0.118 (0.128)	0.0266 (0.0306)	1e-05 (1.71e-05)	0.162 (0.173)	0.0599 (0.0667)	0.0388 (0.044)	0.00866 (0.0105)	0.00246 (0.00317)	0.0114 (0.0135)	0.0102 (0.0122)	0.00047 (0.000653)	0.192 (0.204)
del 2q37 3	52 (10%)	487			1e-05 (1.71e-05)	3e-05 (4.73e-05)	0.00378 (0.00478)	0.0053 (0.00657)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	0.00022 (0.000313)	0.00089 (0.00119)	0.265 (0.278)	0.198 (0.21)
del 20p12 1	35 (6%)	504			1e-05 (1.71e-05)	0.0197 (0.0229)	0.496 (0.512)	0.0041 (0.00515)	0.00822 (0.00995)	0.00258 (0.0033)	0.00018 (0.00026)	0.00536 (0.00663)	0.0447 (0.0503)	0.345 (0.361)
amp 15q26 3	38 (7%)	501			1e-05 (1.71e-05)	0.00394 (0.00497)	0.0472 (0.0531)	0.083 (0.0913)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	9e-05 (0.000134)	1e-05 (1.71e-05)	0.0574 (0.064)	0.0558 (0.0623)
del 2p25 3	26 (5%)	513			1e-05 (1.71e-05)	0.00058 (0.000792)	0.0219 (0.0253)	0.11 (0.12)	2e-05 (3.22e-05)	0.00011 (0.000163)	0.00021 (3e-04)	0.00217 (0.00282)	0.237 (0.249)	0.228 (0.24)
del 3q13 31	43 (8%)	496	0.621 (0.638)	0.184 (0.196)	1e-05 (1.71e-05)	0.0105 (0.0125)	0.0836 (0.0919)	0.00367 (0.00465)	1e-05 (1.71e-05)	1e-05 (1.71e-05)	3e-05 (4.73e-05)	4e-05 (6.19e-05)	0.0523 (0.0585)	0.0664 (0.0737)
amp 10q22 2	143 (27%)	396	0.0209 (0.0242)	0.114 (0.124)	1e-05 (1.71e-05)	0.838 (0.855)	0.125 (0.135)	0.286 (0.299)	0.00012 (0.000177)	0.00236 (0.00305)	0.00089 (0.00119)	0.163 (0.174)	0.00019 (0.000274)	0.213 (0.224)
amp 8p11 22	126 (23%)	413	0.117 (0.127)	0.224 (0.236)	1e-05 (1.71e-05)	0.923 (0.94)	0.445 (0.461)	0.00023 (0.000326)	0.108 (0.118)	0.008 (0.00971)	0.0367 (0.0417)	0.823 (0.84)	0.735 (0.752)	0.115 (0.125)

'amp_1p35.2' versus 'MRNA_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.048

Table S1. Gene #1: 'amp_1p35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 1(1P35.2) MUTATED	1	5	0	0
AMP PEAK 1(1P35.2) WILD-TYPE	14	12	14	7

Figure S1. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p35.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.00074

Table S2. Gene #1: 'amp_1p35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 1(1P35.2) MUTATED	1	5	0	0	0
AMP PEAK 1(1P35.2) WILD-TYPE	13	4	7	7	16

Figure S2. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S3. Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 1(1P35.2) MUTATED	54	0	0	2
AMP PEAK 1(1P35.2) WILD-TYPE	154	178	99	52

Figure S3. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S4. Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 1(1P35.2) MUTATED	30	9	6
AMP PEAK 1(1P35.2) WILD-TYPE	124	69	187

Figure S4. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p35.2' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00022

Table S5. Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 1(1P35.2) MUTATED	1	1	6	8	18	4	7
AMP PEAK 1(1P35.2) WILD-TYPE	38	80	46	48	66	64	46

Figure S5. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p35.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S6. Gene #1: 'amp_1p35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 1(1P35.2) MUTATED	1	34	6	4
AMP PEAK 1(1P35.2) WILD-TYPE	107	148	87	46

Figure S6. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S7. Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 1(1P35.2) MUTATED	46	3	2	4
AMP PEAK 1(1P35.2) WILD-TYPE	142	120	91	129

Figure S7. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S8. Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 1(1P35.2) MUTATED	37	0	7	0	7	4	0
AMP PEAK 1(1P35.2) WILD-TYPE	86	53	40	65	101	62	75

Figure S8. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S9. Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 1(1P35.2) MUTATED	38	2	7	4	2
AMP PEAK 1(1P35.2) WILD-TYPE	126	78	99	129	45

Figure S9. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S10. Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 1(1P35.2) MUTATED	11	38	4
AMP PEAK 1(1P35.2) WILD-TYPE	207	134	136

Figure S10. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00807 (Fisher's exact test), Q value = 0.0098

Table S11. Gene #1: 'amp_1p35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 1(1P35.2) MUTATED	20	5	5	12
AMP PEAK 1(1P35.2) WILD-TYPE	96	93	87	80

Figure S11. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00041

Table S12. Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 1(1P35.2) MUTATED	29	5	8
AMP PEAK 1(1P35.2) WILD-TYPE	134	127	95

Figure S12. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p34.2' versus 'MRNA_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.013

Table S13. Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 2(1P34.2) MUTATED	1	6	0	0
AMP PEAK 2(1P34.2) WILD-TYPE	14	11	14	7

Figure S13. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p34.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00124 (Fisher's exact test), Q value = 0.0016

Table S14. Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 2(1P34.2) MUTATED	2	5	0	0	0
AMP PEAK 2(1P34.2) WILD-TYPE	12	4	7	7	16

Figure S14. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S15. Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 2(1P34.2) MUTATED	70	0	0	3
AMP PEAK 2(1P34.2) WILD-TYPE	138	178	99	51

Figure S15. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S16. Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 2(1P34.2) MUTATED	39	18	6
AMP PEAK 2(1P34.2) WILD-TYPE	115	60	187

Figure S16. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S17. Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 2(1P34.2) MUTATED	1	1	4	14	18	10	8
AMP PEAK 2(1P34.2) WILD-TYPE	38	80	48	42	66	58	45

Figure S17. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S18. Gene #2: 'amp_1p34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 2(1P34.2) MUTATED	0	36	16	4
AMP PEAK 2(1P34.2) WILD-TYPE	108	146	77	46

Figure S18. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S19. Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 2(1P34.2) MUTATED	61	3	3	5
AMP PEAK 2(1P34.2) WILD-TYPE	127	120	90	128

Figure S19. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S20. Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 2(1P34.2) MUTATED	49	0	10	0	8	5	0
AMP PEAK 2(1P34.2) WILD-TYPE	74	53	37	65	100	61	75

Figure S20. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S21. Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 2(1P34.2) MUTATED	59	2	5	4	1
AMP PEAK 2(1P34.2) WILD-TYPE	105	78	101	129	46

Figure S21. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S22. Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 2(1P34.2) MUTATED	12	55	4
AMP PEAK 2(1P34.2) WILD-TYPE	206	117	136

Figure S22. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0031 (Fisher's exact test), Q value = 0.004

Table S23. Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 2(1P34.2) MUTATED	26	6	10	17
AMP PEAK 2(1P34.2) WILD-TYPE	90	92	82	75

Figure S23. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S24. Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 2(1P34.2) MUTATED	40	6	13
AMP PEAK 2(1P34.2) WILD-TYPE	123	126	90

Figure S24. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNA_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.03

Table S25. Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 3(1Q21.3) MUTATED	11	12	6	1
AMP PEAK 3(1Q21.3) WILD-TYPE	4	5	8	6

Figure S25. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00538 (Fisher's exact test), Q value = 0.0066

Table S26. Gene #3: 'amp_1q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 3(1Q21.3) MUTATED	9	7	6	5	3
AMP PEAK 3(1Q21.3) WILD-TYPE	5	2	1	2	13

Figure S26. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S27. Gene #3: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 3(1Q21.3) MUTATED	128	25	37	53
AMP PEAK 3(1Q21.3) WILD-TYPE	80	153	62	1

Figure S27. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.0084

Table S28. Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 3(1Q21.3) MUTATED	82	34	70
AMP PEAK 3(1Q21.3) WILD-TYPE	72	44	123

Figure S28. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.016

Table S29. Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 3(1Q21.3) MUTATED	19	42	15	36	38	30	21
AMP PEAK 3(1Q21.3) WILD-TYPE	20	39	37	20	46	38	32

Figure S29. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.024

Table S30. Gene #3: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 3(1Q21.3) MUTATED	58	91	36	16
AMP PEAK 3(1Q21.3) WILD-TYPE	50	91	57	34

Figure S30. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S31. Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 3(1Q21.3) MUTATED	111	53	41	38
AMP PEAK 3(1Q21.3) WILD-TYPE	77	70	52	95

Figure S31. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S32. Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 3(1Q21.3) MUTATED	82	28	22	32	40	18	21
AMP PEAK 3(1Q21.3) WILD-TYPE	41	25	25	33	68	48	54

Figure S32. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S33. Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 3(1Q21.3) MUTATED	104	45	38	40	13
AMP PEAK 3(1Q21.3) WILD-TYPE	60	35	68	93	34

Figure S33. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S34. Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 3(1Q21.3) MUTATED	92	102	46
AMP PEAK 3(1Q21.3) WILD-TYPE	126	70	94

Figure S34. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S35. Gene #3: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 3(1Q21.3) MUTATED	73	33	40	36
AMP PEAK 3(1Q21.3) WILD-TYPE	43	65	52	56

Figure S35. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S36. Gene #3: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 3(1Q21.3) MUTATED	90	41	51
AMP PEAK 3(1Q21.3) WILD-TYPE	73	91	52

Figure S36. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'MRNA_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.053

Table S37. Gene #4: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 4(1Q22) MUTATED	11	11	6	1
AMP PEAK 4(1Q22) WILD-TYPE	4	6	8	6

Figure S37. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q22' versus 'MRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.013

Table S38. Gene #4: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 4(1Q22) MUTATED	9	6	6	5	3
AMP PEAK 4(1Q22) WILD-TYPE	5	3	1	2	13

Figure S38. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S39. Gene #4: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 4(1Q22) MUTATED	138	26	38	54
AMP PEAK 4(1Q22) WILD-TYPE	70	152	61	0

Figure S39. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0026

Table S40. Gene #4: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 4(1Q22) MUTATED	86	39	72
AMP PEAK 4(1Q22) WILD-TYPE	68	39	121

Figure S40. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'RPPA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.032

Table S41. Gene #4: 'amp_1q22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 4(1Q22) MUTATED	20	43	16	36	40	29	24
AMP PEAK 4(1Q22) WILD-TYPE	19	38	36	20	44	39	29

Figure S41. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.022

Table S42. Gene #4: 'amp_1q22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 4(1Q22) MUTATED	60	94	37	17
AMP PEAK 4(1Q22) WILD-TYPE	48	88	56	33

Figure S42. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S43. Gene #4: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 4(1Q22) MUTATED	119	54	41	42
AMP PEAK 4(1Q22) WILD-TYPE	69	69	52	91

Figure S43. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S44. Gene #4: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 4(1Q22) MUTATED	88	28	23	33	41	20	23
AMP PEAK 4(1Q22) WILD-TYPE	35	25	24	32	67	46	52

Figure S44. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S45. Gene #4: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 4(1Q22) MUTATED	108	45	41	45	14
AMP PEAK 4(1Q22) WILD-TYPE	56	35	65	88	33

Figure S45. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S46. Gene #4: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 4(1Q22) MUTATED	92	110	51
AMP PEAK 4(1Q22) WILD-TYPE	126	62	89

Figure S46. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0026

Table S47. Gene #4: 'amp_1q22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 4(1Q22) MUTATED	73	38	42	40
AMP PEAK 4(1Q22) WILD-TYPE	43	60	50	52

Figure S47. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.00072

Table S48. Gene #4: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 4(1Q22) MUTATED	92	46	55
AMP PEAK 4(1Q22) WILD-TYPE	71	86	48

Figure S48. Get High-res Image Gene #4: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.044

Table S49. Gene #5: 'amp_1q42.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 5(1Q42.3) MUTATED	9	4	5	5	3
AMP PEAK 5(1Q42.3) WILD-TYPE	5	5	2	2	13

Figure S49. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S50. Gene #5: 'amp_1q42.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 5(1Q42.3) MUTATED	109	26	40	52
AMP PEAK 5(1Q42.3) WILD-TYPE	99	152	59	2

Figure S50. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q42.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.036

Table S51. Gene #5: 'amp_1q42.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 5(1Q42.3) MUTATED	57	79	33	16
AMP PEAK 5(1Q42.3) WILD-TYPE	51	103	60	34

Figure S51. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.023

Table S52. Gene #5: 'amp_1q42.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 5(1Q42.3) MUTATED	92	54	39	42
AMP PEAK 5(1Q42.3) WILD-TYPE	96	69	54	91

Figure S52. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 8e-04

Table S53. Gene #5: 'amp_1q42.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 5(1Q42.3) MUTATED	66	29	17	34	38	21	22
AMP PEAK 5(1Q42.3) WILD-TYPE	57	24	30	31	70	45	53

Figure S53. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00044

Table S54. Gene #5: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 5(1Q42.3) MUTATED	82	47	38	43	16
AMP PEAK 5(1Q42.3) WILD-TYPE	82	33	68	90	31

Figure S54. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.038

Table S55. Gene #5: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 5(1Q42.3) MUTATED	94	84	48
AMP PEAK 5(1Q42.3) WILD-TYPE	124	88	92

Figure S55. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0131 (Fisher's exact test), Q value = 0.015

Table S56. Gene #5: 'amp_1q42.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 5(1Q42.3) MUTATED	73	42	51
AMP PEAK 5(1Q42.3) WILD-TYPE	90	90	52

Figure S56. Get High-res Image Gene #5: 'amp_1q42.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S57. Gene #6: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 6(2P24.3) MUTATED	91	6	18	7
AMP PEAK 6(2P24.3) WILD-TYPE	117	172	81	47

Figure S57. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S58. Gene #6: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 6(2P24.3) MUTATED	55	21	21
AMP PEAK 6(2P24.3) WILD-TYPE	99	57	172

Figure S58. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S59. Gene #6: 'amp_2p24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 6(2P24.3) MUTATED	4	6	12	18	30	16	15
AMP PEAK 6(2P24.3) WILD-TYPE	35	75	40	38	54	52	38

Figure S59. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S60. Gene #6: 'amp_2p24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 6(2P24.3) MUTATED	12	61	19	9
AMP PEAK 6(2P24.3) WILD-TYPE	96	121	74	41

Figure S60. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S61. Gene #6: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 6(2P24.3) MUTATED	74	16	17	15
AMP PEAK 6(2P24.3) WILD-TYPE	114	107	76	118

Figure S61. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S62. Gene #6: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 6(2P24.3) MUTATED	59	7	14	6	19	11	6
AMP PEAK 6(2P24.3) WILD-TYPE	64	46	33	59	89	55	69

Figure S62. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S63. Gene #6: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 6(2P24.3) MUTATED	67	11	18	16	8
AMP PEAK 6(2P24.3) WILD-TYPE	97	69	88	117	39

Figure S63. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S64. Gene #6: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 6(2P24.3) MUTATED	31	72	17
AMP PEAK 6(2P24.3) WILD-TYPE	187	100	123

Figure S64. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S65. Gene #6: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 6(2P24.3) MUTATED	44	11	17	21
AMP PEAK 6(2P24.3) WILD-TYPE	72	87	75	71

Figure S65. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00057

Table S66. Gene #6: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 6(2P24.3) MUTATED	51	16	26
AMP PEAK 6(2P24.3) WILD-TYPE	112	116	77

Figure S66. Get High-res Image Gene #6: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q13' versus 'MRNA_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.033

Table S67. Gene #7: 'amp_2q13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 7(2Q13) MUTATED	3	5	1	0	1
AMP PEAK 7(2Q13) WILD-TYPE	11	4	6	7	15

Figure S67. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S68. Gene #7: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 7(2Q13) MUTATED	96	1	16	6
AMP PEAK 7(2Q13) WILD-TYPE	112	177	83	48

Figure S68. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S69. Gene #7: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 7(2Q13) MUTATED	59	26	11
AMP PEAK 7(2Q13) WILD-TYPE	95	52	182

Figure S69. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q13' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S70. Gene #7: 'amp_2q13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 7(2Q13) MUTATED	4	4	7	20	31	16	17
AMP PEAK 7(2Q13) WILD-TYPE	35	77	45	36	53	52	36

Figure S70. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2q13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S71. Gene #7: 'amp_2q13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 7(2Q13) MUTATED	9	61	19	10
AMP PEAK 7(2Q13) WILD-TYPE	99	121	74	40

Figure S71. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2q13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S72. Gene #7: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 7(2Q13) MUTATED	86	10	14	8
AMP PEAK 7(2Q13) WILD-TYPE	102	113	79	125

Figure S72. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S73. Gene #7: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 7(2Q13) MUTATED	73	5	13	2	15	6	4
AMP PEAK 7(2Q13) WILD-TYPE	50	48	34	63	93	60	71

Figure S73. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S74. Gene #7: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 7(2Q13) MUTATED	74	7	19	8	9
AMP PEAK 7(2Q13) WILD-TYPE	90	73	87	125	38

Figure S74. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S75. Gene #7: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 7(2Q13) MUTATED	24	83	10
AMP PEAK 7(2Q13) WILD-TYPE	194	89	130

Figure S75. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S76. Gene #7: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 7(2Q13) MUTATED	43	7	19	25
AMP PEAK 7(2Q13) WILD-TYPE	73	91	73	67

Figure S76. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S77. Gene #7: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 7(2Q13) MUTATED	54	9	31
AMP PEAK 7(2Q13) WILD-TYPE	109	123	72

Figure S77. Get High-res Image Gene #7: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S78. Gene #8: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 8(3P25.1) MUTATED	70	1	9	2
AMP PEAK 8(3P25.1) WILD-TYPE	138	177	90	52

Figure S78. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S79. Gene #8: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 8(3P25.1) MUTATED	38	19	11
AMP PEAK 8(3P25.1) WILD-TYPE	116	59	182

Figure S79. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'RPPA_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.00088

Table S80. Gene #8: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 8(3P25.1) MUTATED	2	5	4	16	20	10	6
AMP PEAK 8(3P25.1) WILD-TYPE	37	76	48	40	64	58	47

Figure S80. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3p25.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S81. Gene #8: 'amp_3p25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 8(3P25.1) MUTATED	6	44	9	4
AMP PEAK 8(3P25.1) WILD-TYPE	102	138	84	46

Figure S81. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S82. Gene #8: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 8(3P25.1) MUTATED	62	4	8	8
AMP PEAK 8(3P25.1) WILD-TYPE	126	119	85	125

Figure S82. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S83. Gene #8: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 8(3P25.1) MUTATED	41	0	13	4	15	5	4
AMP PEAK 8(3P25.1) WILD-TYPE	82	53	34	61	93	61	71

Figure S83. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S84. Gene #8: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 8(3P25.1) MUTATED	50	4	10	11	5
AMP PEAK 8(3P25.1) WILD-TYPE	114	76	96	122	42

Figure S84. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S85. Gene #8: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 8(3P25.1) MUTATED	18	50	12
AMP PEAK 8(3P25.1) WILD-TYPE	200	122	128

Figure S85. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.0042

Table S86. Gene #8: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 8(3P25.1) MUTATED	27	6	18	14
AMP PEAK 8(3P25.1) WILD-TYPE	89	92	74	78

Figure S86. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00454 (Fisher's exact test), Q value = 0.0057

Table S87. Gene #8: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 8(3P25.1) MUTATED	36	11	18
AMP PEAK 8(3P25.1) WILD-TYPE	127	121	85

Figure S87. Get High-res Image Gene #8: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S88. Gene #9: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 9(3P14.1) MUTATED	55	1	8	1
AMP PEAK 9(3P14.1) WILD-TYPE	153	177	91	53

Figure S88. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p14.1' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00034

Table S89. Gene #9: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 9(3P14.1) MUTATED	31	13	12
AMP PEAK 9(3P14.1) WILD-TYPE	123	65	181

Figure S89. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.022

Table S90. Gene #9: 'amp_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 9(3P14.1) MUTATED	5	28	12	3
AMP PEAK 9(3P14.1) WILD-TYPE	103	154	81	47

Figure S90. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S91. Gene #9: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 9(3P14.1) MUTATED	46	3	7	9
AMP PEAK 9(3P14.1) WILD-TYPE	142	120	86	124

Figure S91. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S92. Gene #9: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 9(3P14.1) MUTATED	29	0	9	4	14	4	5
AMP PEAK 9(3P14.1) WILD-TYPE	94	53	38	61	94	62	70

Figure S92. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S93. Gene #9: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 9(3P14.1) MUTATED	37	3	10	10	4
AMP PEAK 9(3P14.1) WILD-TYPE	127	77	96	123	43

Figure S93. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00061

Table S94. Gene #9: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 9(3P14.1) MUTATED	17	35	12
AMP PEAK 9(3P14.1) WILD-TYPE	201	137	128

Figure S94. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.016

Table S95. Gene #9: 'amp_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 9(3P14.1) MUTATED	21	5	16	10
AMP PEAK 9(3P14.1) WILD-TYPE	95	93	76	82

Figure S95. Get High-res Image Gene #9: 'amp_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S96. Gene #10: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 10(3Q26.2) MUTATED	1	11	1	0
AMP PEAK 10(3Q26.2) WILD-TYPE	14	6	13	7

Figure S96. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S97. Gene #10: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 10(3Q26.2) MUTATED	4	8	1	0	0
AMP PEAK 10(3Q26.2) WILD-TYPE	10	1	6	7	16

Figure S97. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S98. Gene #10: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 10(3Q26.2) MUTATED	154	2	12	7
AMP PEAK 10(3Q26.2) WILD-TYPE	54	176	87	47

Figure S98. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S99. Gene #10: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 10(3Q26.2) MUTATED	88	36	26
AMP PEAK 10(3Q26.2) WILD-TYPE	66	42	167

Figure S99. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S100. Gene #10: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 10(3Q26.2) MUTATED	5	7	12	27	42	24	17
AMP PEAK 10(3Q26.2) WILD-TYPE	34	74	40	29	42	44	36

Figure S100. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S101. Gene #10: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 10(3Q26.2) MUTATED	10	80	32	12
AMP PEAK 10(3Q26.2) WILD-TYPE	98	102	61	38

Figure S101. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S102. Gene #10: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 10(3Q26.2) MUTATED	126	5	23	20
AMP PEAK 10(3Q26.2) WILD-TYPE	62	118	70	113

Figure S102. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S103. Gene #10: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 10(3Q26.2) MUTATED	95	0	26	5	26	14	8
AMP PEAK 10(3Q26.2) WILD-TYPE	28	53	21	60	82	52	67

Figure S103. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S104. Gene #10: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 10(3Q26.2) MUTATED	111	7	21	20	12
AMP PEAK 10(3Q26.2) WILD-TYPE	53	73	85	113	35

Figure S104. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S105. Gene #10: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 10(3Q26.2) MUTATED	37	111	23
AMP PEAK 10(3Q26.2) WILD-TYPE	181	61	117

Figure S105. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S106. Gene #10: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 10(3Q26.2) MUTATED	61	18	29	35
AMP PEAK 10(3Q26.2) WILD-TYPE	55	80	63	57

Figure S106. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S107. Gene #10: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 10(3Q26.2) MUTATED	78	25	40
AMP PEAK 10(3Q26.2) WILD-TYPE	85	107	63

Figure S107. Get High-res Image Gene #10: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.00063

Table S108. Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 11(3Q26.2) MUTATED	1	10	1	0
AMP PEAK 11(3Q26.2) WILD-TYPE	14	7	13	7

Figure S108. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S109. Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 11(3Q26.2) MUTATED	3	8	1	0	0
AMP PEAK 11(3Q26.2) WILD-TYPE	11	1	6	7	16

Figure S109. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S110. Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 11(3Q26.2) MUTATED	147	1	11	5
AMP PEAK 11(3Q26.2) WILD-TYPE	61	177	88	49

Figure S110. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S111. Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 11(3Q26.2) MUTATED	85	34	22
AMP PEAK 11(3Q26.2) WILD-TYPE	69	44	171

Figure S111. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S112. Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 11(3Q26.2) MUTATED	5	6	12	24	42	22	17
AMP PEAK 11(3Q26.2) WILD-TYPE	34	75	40	32	42	46	36

Figure S112. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S113. Gene #11: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 11(3Q26.2) MUTATED	8	77	30	13
AMP PEAK 11(3Q26.2) WILD-TYPE	100	105	63	37

Figure S113. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S114. Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 11(3Q26.2) MUTATED	120	6	20	17
AMP PEAK 11(3Q26.2) WILD-TYPE	68	117	73	116

Figure S114. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S115. Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 11(3Q26.2) MUTATED	92	0	24	5	24	11	7
AMP PEAK 11(3Q26.2) WILD-TYPE	31	53	23	60	84	55	68

Figure S115. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S116. Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 11(3Q26.2) MUTATED	106	6	19	18	11
AMP PEAK 11(3Q26.2) WILD-TYPE	58	74	87	115	36

Figure S116. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S117. Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 11(3Q26.2) MUTATED	35	106	19
AMP PEAK 11(3Q26.2) WILD-TYPE	183	66	121

Figure S117. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S118. Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 11(3Q26.2) MUTATED	59	15	26	34
AMP PEAK 11(3Q26.2) WILD-TYPE	57	83	66	58

Figure S118. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S119. Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 11(3Q26.2) MUTATED	77	19	38
AMP PEAK 11(3Q26.2) WILD-TYPE	86	113	65

Figure S119. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNA_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.048

Table S120. Gene #12: 'amp_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 12(4P16.3) MUTATED	1	5	0	0
AMP PEAK 12(4P16.3) WILD-TYPE	14	12	14	7

Figure S120. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.0092

Table S121. Gene #12: 'amp_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 12(4P16.3) MUTATED	2	4	0	0	0
AMP PEAK 12(4P16.3) WILD-TYPE	12	5	7	7	16

Figure S121. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S122. Gene #12: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 12(4P16.3) MUTATED	49	2	0	1
AMP PEAK 12(4P16.3) WILD-TYPE	159	176	99	53

Figure S122. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S123. Gene #12: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 12(4P16.3) MUTATED	18	19	6
AMP PEAK 12(4P16.3) WILD-TYPE	136	59	187

Figure S123. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'RPPA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00023

Table S124. Gene #12: 'amp_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 12(4P16.3) MUTATED	1	1	2	12	14	6	4
AMP PEAK 12(4P16.3) WILD-TYPE	38	80	50	44	70	62	49

Figure S124. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S125. Gene #12: 'amp_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 12(4P16.3) MUTATED	1	30	8	1
AMP PEAK 12(4P16.3) WILD-TYPE	107	152	85	49

Figure S125. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S126. Gene #12: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 12(4P16.3) MUTATED	46	3	0	2
AMP PEAK 12(4P16.3) WILD-TYPE	142	120	93	131

Figure S126. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S127. Gene #12: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 12(4P16.3) MUTATED	39	0	3	0	8	0	1
AMP PEAK 12(4P16.3) WILD-TYPE	84	53	44	65	100	66	74

Figure S127. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S128. Gene #12: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 12(4P16.3) MUTATED	39	1	4	4	2
AMP PEAK 12(4P16.3) WILD-TYPE	125	79	102	129	45

Figure S128. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S129. Gene #12: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 12(4P16.3) MUTATED	7	39	4
AMP PEAK 12(4P16.3) WILD-TYPE	211	133	136

Figure S129. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00616 (Fisher's exact test), Q value = 0.0076

Table S130. Gene #12: 'amp_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 12(4P16.3) MUTATED	22	5	7	7
AMP PEAK 12(4P16.3) WILD-TYPE	94	93	85	85

Figure S130. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0014

Table S131. Gene #12: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 12(4P16.3) MUTATED	27	5	9
AMP PEAK 12(4P16.3) WILD-TYPE	136	127	94

Figure S131. Get High-res Image Gene #12: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.05

Table S132. Gene #13: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 13(5P15.33) MUTATED	2	4	1	1	0
AMP PEAK 13(5P15.33) WILD-TYPE	12	5	6	6	16

Figure S132. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S133. Gene #13: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 13(5P15.33) MUTATED	83	0	3	3
AMP PEAK 13(5P15.33) WILD-TYPE	125	178	96	51

Figure S133. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S134. Gene #13: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 13(5P15.33) MUTATED	51	17	8
AMP PEAK 13(5P15.33) WILD-TYPE	103	61	185

Figure S134. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S135. Gene #13: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 13(5P15.33) MUTATED	0	6	5	16	26	12	9
AMP PEAK 13(5P15.33) WILD-TYPE	39	75	47	40	58	56	44

Figure S135. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S136. Gene #13: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 13(5P15.33) MUTATED	5	50	15	4
AMP PEAK 13(5P15.33) WILD-TYPE	103	132	78	46

Figure S136. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S137. Gene #13: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 13(5P15.33) MUTATED	73	7	6	2
AMP PEAK 13(5P15.33) WILD-TYPE	115	116	87	131

Figure S137. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S138. Gene #13: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 13(5P15.33) MUTATED	54	3	13	2	11	5	0
AMP PEAK 13(5P15.33) WILD-TYPE	69	50	34	63	97	61	75

Figure S138. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S139. Gene #13: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 13(5P15.33) MUTATED	61	6	10	5	6
AMP PEAK 13(5P15.33) WILD-TYPE	103	74	96	128	41

Figure S139. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S140. Gene #13: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 13(5P15.33) MUTATED	22	61	5
AMP PEAK 13(5P15.33) WILD-TYPE	196	111	135

Figure S140. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S141. Gene #13: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 13(5P15.33) MUTATED	41	3	15	16
AMP PEAK 13(5P15.33) WILD-TYPE	75	95	77	76

Figure S141. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S142. Gene #13: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 13(5P15.33) MUTATED	48	8	19
AMP PEAK 13(5P15.33) WILD-TYPE	115	124	84

Figure S142. Get High-res Image Gene #13: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S143. Gene #14: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 14(5Q35.3) MUTATED	54	0	1	2
AMP PEAK 14(5Q35.3) WILD-TYPE	154	178	98	52

Figure S143. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S144. Gene #14: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 14(5Q35.3) MUTATED	27	16	7
AMP PEAK 14(5Q35.3) WILD-TYPE	127	62	186

Figure S144. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S145. Gene #14: 'amp_5q35.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 14(5Q35.3) MUTATED	1	3	3	7	23	5	4
AMP PEAK 14(5Q35.3) WILD-TYPE	38	78	49	49	61	63	49

Figure S145. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.00049

Table S146. Gene #14: 'amp_5q35.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 14(5Q35.3) MUTATED	4	33	7	2
AMP PEAK 14(5Q35.3) WILD-TYPE	104	149	86	48

Figure S146. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S147. Gene #14: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 14(5Q35.3) MUTATED	45	3	6	3
AMP PEAK 14(5Q35.3) WILD-TYPE	143	120	87	130

Figure S147. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S148. Gene #14: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 14(5Q35.3) MUTATED	35	2	9	1	7	2	1
AMP PEAK 14(5Q35.3) WILD-TYPE	88	51	38	64	101	64	74

Figure S148. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S149. Gene #14: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 14(5Q35.3) MUTATED	40	5	5	4	2
AMP PEAK 14(5Q35.3) WILD-TYPE	124	75	101	129	45

Figure S149. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S150. Gene #14: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 14(5Q35.3) MUTATED	10	42	4
AMP PEAK 14(5Q35.3) WILD-TYPE	208	130	136

Figure S150. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.00094

Table S151. Gene #14: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 14(5Q35.3) MUTATED	27	5	16
AMP PEAK 14(5Q35.3) WILD-TYPE	136	127	87

Figure S151. Get High-res Image Gene #14: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p24.2' versus 'MRNA_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.0059

Table S152. Gene #15: 'amp_6p24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 15(6P24.2) MUTATED	1	9	2	0
AMP PEAK 15(6P24.2) WILD-TYPE	14	8	12	7

Figure S152. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p24.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.00079

Table S153. Gene #15: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 15(6P24.2) MUTATED	3	7	0	0	2
AMP PEAK 15(6P24.2) WILD-TYPE	11	2	7	7	14

Figure S153. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S154. Gene #15: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 15(6P24.2) MUTATED	105	4	5	3
AMP PEAK 15(6P24.2) WILD-TYPE	103	174	94	51

Figure S154. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S155. Gene #15: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 15(6P24.2) MUTATED	61	24	15
AMP PEAK 15(6P24.2) WILD-TYPE	93	54	178

Figure S155. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p24.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S156. Gene #15: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 15(6P24.2) MUTATED	2	6	5	22	29	11	11
AMP PEAK 15(6P24.2) WILD-TYPE	37	75	47	34	55	57	42

Figure S156. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p24.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S157. Gene #15: 'amp_6p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 15(6P24.2) MUTATED	5	57	18	6
AMP PEAK 15(6P24.2) WILD-TYPE	103	125	75	44

Figure S157. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S158. Gene #15: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 15(6P24.2) MUTATED	89	6	7	15
AMP PEAK 15(6P24.2) WILD-TYPE	99	117	86	118

Figure S158. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S159. Gene #15: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 15(6P24.2) MUTATED	68	0	11	5	19	8	6
AMP PEAK 15(6P24.2) WILD-TYPE	55	53	36	60	89	58	69

Figure S159. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S160. Gene #15: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 15(6P24.2) MUTATED	75	6	11	12	10
AMP PEAK 15(6P24.2) WILD-TYPE	89	74	95	121	37

Figure S160. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S161. Gene #15: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 15(6P24.2) MUTATED	25	77	12
AMP PEAK 15(6P24.2) WILD-TYPE	193	95	128

Figure S161. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S162. Gene #15: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 15(6P24.2) MUTATED	49	10	20	17
AMP PEAK 15(6P24.2) WILD-TYPE	67	88	72	75

Figure S162. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S163. Gene #15: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 15(6P24.2) MUTATED	55	15	26
AMP PEAK 15(6P24.2) WILD-TYPE	108	117	77

Figure S163. Get High-res Image Gene #15: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S164. Gene #16: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 16(6Q25.1) MUTATED	78	3	6	1
AMP PEAK 16(6Q25.1) WILD-TYPE	130	175	93	53

Figure S164. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S165. Gene #16: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 16(6Q25.1) MUTATED	51	12	16
AMP PEAK 16(6Q25.1) WILD-TYPE	103	66	177

Figure S165. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'RPPA_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.0047

Table S166. Gene #16: 'amp_6q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 16(6Q25.1) MUTATED	3	5	6	11	24	11	7
AMP PEAK 16(6Q25.1) WILD-TYPE	36	76	46	45	60	57	46

Figure S166. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S167. Gene #16: 'amp_6q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 16(6Q25.1) MUTATED	4	41	17	5
AMP PEAK 16(6Q25.1) WILD-TYPE	104	141	76	45

Figure S167. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S168. Gene #16: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 16(6Q25.1) MUTATED	56	7	7	17
AMP PEAK 16(6Q25.1) WILD-TYPE	132	116	86	116

Figure S168. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S169. Gene #16: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 16(6Q25.1) MUTATED	40	0	9	6	15	11	6
AMP PEAK 16(6Q25.1) WILD-TYPE	83	53	38	59	93	55	69

Figure S169. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S170. Gene #16: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 16(6Q25.1) MUTATED	48	9	10	12	9
AMP PEAK 16(6Q25.1) WILD-TYPE	116	71	96	121	38

Figure S170. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S171. Gene #16: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 16(6Q25.1) MUTATED	26	50	12
AMP PEAK 16(6Q25.1) WILD-TYPE	192	122	128

Figure S171. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.013

Table S172. Gene #16: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 16(6Q25.1) MUTATED	32	10	15	19
AMP PEAK 16(6Q25.1) WILD-TYPE	84	88	77	73

Figure S172. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.021

Table S173. Gene #16: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 16(6Q25.1) MUTATED	41	16	19
AMP PEAK 16(6Q25.1) WILD-TYPE	122	116	84

Figure S173. Get High-res Image Gene #16: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S174. Gene #17: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 17(7Q31.2) MUTATED	62	4	18	9
AMP PEAK 17(7Q31.2) WILD-TYPE	146	174	81	45

Figure S174. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00056

Table S175. Gene #17: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 17(7Q31.2) MUTATED	42	10	22
AMP PEAK 17(7Q31.2) WILD-TYPE	112	68	171

Figure S175. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0017

Table S176. Gene #17: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 17(7Q31.2) MUTATED	8	44	12	6
AMP PEAK 17(7Q31.2) WILD-TYPE	100	138	81	44

Figure S176. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0013

Table S177. Gene #17: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 17(7Q31.2) MUTATED	50	15	12	16
AMP PEAK 17(7Q31.2) WILD-TYPE	138	108	81	117

Figure S177. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00018

Table S178. Gene #17: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 17(7Q31.2) MUTATED	34	8	13	2	19	10	7
AMP PEAK 17(7Q31.2) WILD-TYPE	89	45	34	63	89	56	68

Figure S178. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00072

Table S179. Gene #17: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 17(7Q31.2) MUTATED	46	15	11	15	6
AMP PEAK 17(7Q31.2) WILD-TYPE	118	65	95	118	41

Figure S179. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 0.006

Table S180. Gene #17: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 17(7Q31.2) MUTATED	34	43	16
AMP PEAK 17(7Q31.2) WILD-TYPE	184	129	124

Figure S180. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.003

Table S181. Gene #17: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 17(7Q31.2) MUTATED	32	8	18	14
AMP PEAK 17(7Q31.2) WILD-TYPE	84	90	74	78

Figure S181. Get High-res Image Gene #17: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S182. Gene #18: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 18(8P11.22) MUTATED	74	7	41	4
AMP PEAK 18(8P11.22) WILD-TYPE	134	171	58	50

Figure S182. Get High-res Image Gene #18: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00033

Table S183. Gene #18: 'amp_8p11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 18(8P11.22) MUTATED	15	37	37	13
AMP PEAK 18(8P11.22) WILD-TYPE	93	145	56	37

Figure S183. Get High-res Image Gene #18: 'amp_8p11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.008 (Fisher's exact test), Q value = 0.0097

Table S184. Gene #18: 'amp_8p11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 18(8P11.22) MUTATED	30	9	9	9	36	22	11
AMP PEAK 18(8P11.22) WILD-TYPE	93	44	38	56	72	44	64

Figure S184. Get High-res Image Gene #18: 'amp_8p11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.22' versus 'MIRSEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.042

Table S185. Gene #18: 'amp_8p11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 18(8P11.22) MUTATED	47	23	15	31	8
AMP PEAK 18(8P11.22) WILD-TYPE	117	57	91	102	39

Figure S185. Get High-res Image Gene #18: 'amp_8p11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MRNA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.02

Table S186. Gene #19: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 19(8P11.21) MUTATED	1	8	2	0
AMP PEAK 19(8P11.21) WILD-TYPE	14	9	12	7

Figure S186. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.034

Table S187. Gene #19: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 19(8P11.21) MUTATED	4	5	0	0	2
AMP PEAK 19(8P11.21) WILD-TYPE	10	4	7	7	14

Figure S187. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S188. Gene #19: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 19(8P11.21) MUTATED	109	6	41	6
AMP PEAK 19(8P11.21) WILD-TYPE	99	172	58	48

Figure S188. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.014

Table S189. Gene #19: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 19(8P11.21) MUTATED	62	27	49
AMP PEAK 19(8P11.21) WILD-TYPE	92	51	144

Figure S189. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.002

Table S190. Gene #19: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 19(8P11.21) MUTATED	8	13	13	23	37	18	17
AMP PEAK 19(8P11.21) WILD-TYPE	31	68	39	33	47	50	36

Figure S190. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S191. Gene #19: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 19(8P11.21) MUTATED	15	58	39	17
AMP PEAK 19(8P11.21) WILD-TYPE	93	124	54	33

Figure S191. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S192. Gene #19: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 19(8P11.21) MUTATED	86	28	18	30
AMP PEAK 19(8P11.21) WILD-TYPE	102	95	75	103

Figure S192. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S193. Gene #19: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 19(8P11.21) MUTATED	59	9	19	10	34	20	11
AMP PEAK 19(8P11.21) WILD-TYPE	64	44	28	55	74	46	64

Figure S193. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S194. Gene #19: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 19(8P11.21) MUTATED	79	22	17	30	11
AMP PEAK 19(8P11.21) WILD-TYPE	85	58	89	103	36

Figure S194. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S195. Gene #19: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 19(8P11.21) MUTATED	54	74	31
AMP PEAK 19(8P11.21) WILD-TYPE	164	98	109

Figure S195. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0015

Table S196. Gene #19: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 19(8P11.21) MUTATED	55	23	27	26
AMP PEAK 19(8P11.21) WILD-TYPE	61	75	65	66

Figure S196. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00385 (Fisher's exact test), Q value = 0.0049

Table S197. Gene #19: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 19(8P11.21) MUTATED	69	33	29
AMP PEAK 19(8P11.21) WILD-TYPE	94	99	74

Figure S197. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.027

Table S198. Gene #20: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 20(8Q24.21) MUTATED	1	8	3	0
AMP PEAK 20(8Q24.21) WILD-TYPE	14	9	11	7

Figure S198. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S199. Gene #20: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 20(8Q24.21) MUTATED	151	8	44	6
AMP PEAK 20(8Q24.21) WILD-TYPE	57	170	55	48

Figure S199. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S200. Gene #20: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 20(8Q24.21) MUTATED	88	39	54
AMP PEAK 20(8Q24.21) WILD-TYPE	66	39	139

Figure S200. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S201. Gene #20: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 20(8Q24.21) MUTATED	9	14	15	28	47	25	25
AMP PEAK 20(8Q24.21) WILD-TYPE	30	67	37	28	37	43	28

Figure S201. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S202. Gene #20: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 20(8Q24.21) MUTATED	16	82	44	21
AMP PEAK 20(8Q24.21) WILD-TYPE	92	100	49	29

Figure S202. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S203. Gene #20: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 20(8Q24.21) MUTATED	119	31	24	34
AMP PEAK 20(8Q24.21) WILD-TYPE	69	92	69	99

Figure S203. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S204. Gene #20: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 20(8Q24.21) MUTATED	86	10	27	8	39	26	12
AMP PEAK 20(8Q24.21) WILD-TYPE	37	43	20	57	69	40	63

Figure S204. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S205. Gene #20: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 20(8Q24.21) MUTATED	110	23	22	35	16
AMP PEAK 20(8Q24.21) WILD-TYPE	54	57	84	98	31

Figure S205. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S206. Gene #20: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 20(8Q24.21) MUTATED	62	109	35
AMP PEAK 20(8Q24.21) WILD-TYPE	156	63	105

Figure S206. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S207. Gene #20: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 20(8Q24.21) MUTATED	70	26	35	38
AMP PEAK 20(8Q24.21) WILD-TYPE	46	72	57	54

Figure S207. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S208. Gene #20: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 20(8Q24.21) MUTATED	90	35	44
AMP PEAK 20(8Q24.21) WILD-TYPE	73	97	59

Figure S208. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.0054

Table S209. Gene #21: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 21(8Q24.21) MUTATED	1	9	2	0
AMP PEAK 21(8Q24.21) WILD-TYPE	14	8	12	7

Figure S209. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00611 (Fisher's exact test), Q value = 0.0075

Table S210. Gene #21: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 21(8Q24.21) MUTATED	4	6	0	0	2
AMP PEAK 21(8Q24.21) WILD-TYPE	10	3	7	7	14

Figure S210. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S211. Gene #21: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 21(8Q24.21) MUTATED	152	13	43	7
AMP PEAK 21(8Q24.21) WILD-TYPE	56	165	56	47

Figure S211. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S212. Gene #21: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 21(8Q24.21) MUTATED	87	39	59
AMP PEAK 21(8Q24.21) WILD-TYPE	67	39	134

Figure S212. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S213. Gene #21: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 21(8Q24.21) MUTATED	9	13	16	28	51	25	28
AMP PEAK 21(8Q24.21) WILD-TYPE	30	68	36	28	33	43	25

Figure S213. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S214. Gene #21: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 21(8Q24.21) MUTATED	16	85	45	24
AMP PEAK 21(8Q24.21) WILD-TYPE	92	97	48	26

Figure S214. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S215. Gene #21: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 21(8Q24.21) MUTATED	124	32	23	35
AMP PEAK 21(8Q24.21) WILD-TYPE	64	91	70	98

Figure S215. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S216. Gene #21: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 21(8Q24.21) MUTATED	91	11	25	9	39	25	14
AMP PEAK 21(8Q24.21) WILD-TYPE	32	42	22	56	69	41	61

Figure S216. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S217. Gene #21: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 21(8Q24.21) MUTATED	112	24	23	36	16
AMP PEAK 21(8Q24.21) WILD-TYPE	52	56	83	97	31

Figure S217. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S218. Gene #21: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 21(8Q24.21) MUTATED	64	109	38
AMP PEAK 21(8Q24.21) WILD-TYPE	154	63	102

Figure S218. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S219. Gene #21: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 21(8Q24.21) MUTATED	72	29	34	39
AMP PEAK 21(8Q24.21) WILD-TYPE	44	69	58	53

Figure S219. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S220. Gene #21: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 21(8Q24.21) MUTATED	94	39	41
AMP PEAK 21(8Q24.21) WILD-TYPE	69	93	62

Figure S220. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S221. Gene #22: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 22(9P24.2) MUTATED	60	4	1	0
AMP PEAK 22(9P24.2) WILD-TYPE	148	174	98	54

Figure S221. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S222. Gene #22: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 22(9P24.2) MUTATED	35	12	7
AMP PEAK 22(9P24.2) WILD-TYPE	119	66	186

Figure S222. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p24.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S223. Gene #22: 'amp_9p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 22(9P24.2) MUTATED	1	1	4	16	23	7	3
AMP PEAK 22(9P24.2) WILD-TYPE	38	80	48	40	61	61	50

Figure S223. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9p24.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S224. Gene #22: 'amp_9p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 22(9P24.2) MUTATED	1	38	15	1
AMP PEAK 22(9P24.2) WILD-TYPE	107	144	78	49

Figure S224. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S225. Gene #22: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 22(9P24.2) MUTATED	53	4	5	3
AMP PEAK 22(9P24.2) WILD-TYPE	135	119	88	130

Figure S225. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S226. Gene #22: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 22(9P24.2) MUTATED	41	0	6	2	12	4	0
AMP PEAK 22(9P24.2) WILD-TYPE	82	53	41	63	96	62	75

Figure S226. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S227. Gene #22: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 22(9P24.2) MUTATED	49	5	7	2	1
AMP PEAK 22(9P24.2) WILD-TYPE	115	75	99	131	46

Figure S227. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S228. Gene #22: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 22(9P24.2) MUTATED	18	43	3
AMP PEAK 22(9P24.2) WILD-TYPE	200	129	137

Figure S228. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00056

Table S229. Gene #22: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 22(9P24.2) MUTATED	28	5	9	10
AMP PEAK 22(9P24.2) WILD-TYPE	88	93	83	82

Figure S229. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00033

Table S230. Gene #22: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 22(9P24.2) MUTATED	32	6	14
AMP PEAK 22(9P24.2) WILD-TYPE	131	126	89

Figure S230. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.016

Table S231. Gene #23: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 23(9Q34.3) MUTATED	0	4	1	0	1
AMP PEAK 23(9Q34.3) WILD-TYPE	14	5	6	7	15

Figure S231. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S232. Gene #23: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 23(9Q34.3) MUTATED	36	1	1	1
AMP PEAK 23(9Q34.3) WILD-TYPE	172	177	98	53

Figure S232. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S233. Gene #23: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 23(9Q34.3) MUTATED	18	10	2
AMP PEAK 23(9Q34.3) WILD-TYPE	136	68	191

Figure S233. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.013

Table S234. Gene #23: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 23(9Q34.3) MUTATED	1	1	1	6	12	6	5
AMP PEAK 23(9Q34.3) WILD-TYPE	38	80	51	50	72	62	48

Figure S234. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.0027

Table S235. Gene #23: 'amp_9q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 23(9Q34.3) MUTATED	1	22	6	3
AMP PEAK 23(9Q34.3) WILD-TYPE	107	160	87	47

Figure S235. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S236. Gene #23: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 23(9Q34.3) MUTATED	33	3	1	1
AMP PEAK 23(9Q34.3) WILD-TYPE	155	120	92	132

Figure S236. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S237. Gene #23: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 23(9Q34.3) MUTATED	30	2	2	0	2	2	0
AMP PEAK 23(9Q34.3) WILD-TYPE	93	51	45	65	106	64	75

Figure S237. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S238. Gene #23: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 23(9Q34.3) MUTATED	24	3	4	2	2
AMP PEAK 23(9Q34.3) WILD-TYPE	140	77	102	131	45

Figure S238. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S239. Gene #23: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 23(9Q34.3) MUTATED	7	26	2
AMP PEAK 23(9Q34.3) WILD-TYPE	211	146	138

Figure S239. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.0096

Table S240. Gene #23: 'amp_9q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 23(9Q34.3) MUTATED	18	3	9
AMP PEAK 23(9Q34.3) WILD-TYPE	145	129	94

Figure S240. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'MRNA_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.024

Table S241. Gene #24: 'amp_10q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 24(10Q22.2) MUTATED	2	7	9	1
AMP PEAK 24(10Q22.2) WILD-TYPE	13	10	5	6

Figure S241. Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S242. Gene #24: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 24(10Q22.2) MUTATED	80	25	26	12
AMP PEAK 24(10Q22.2) WILD-TYPE	128	153	73	42

Figure S242. Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00018

Table S243. Gene #24: 'amp_10q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 24(10Q22.2) MUTATED	67	30	10	35
AMP PEAK 24(10Q22.2) WILD-TYPE	121	93	83	98

Figure S243. Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.003

Table S244. Gene #24: 'amp_10q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 24(10Q22.2) MUTATED	49	15	10	10	22	21	15
AMP PEAK 24(10Q22.2) WILD-TYPE	74	38	37	55	86	45	60

Figure S244. Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0012

Table S245. Gene #24: 'amp_10q22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 24(10Q22.2) MUTATED	62	14	18	36	11
AMP PEAK 24(10Q22.2) WILD-TYPE	102	66	88	97	36

Figure S245. Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00027

Table S246. Gene #24: 'amp_10q22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 24(10Q22.2) MUTATED	37	31	22	8
AMP PEAK 24(10Q22.2) WILD-TYPE	79	67	70	84

Figure S246. Get High-res Image Gene #24: 'amp_10q22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MRNA_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0034

Table S247. Gene #25: 'amp_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 25(11P11.2) MUTATED	0	6	0	0
AMP PEAK 25(11P11.2) WILD-TYPE	15	11	14	7

Figure S247. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00796 (Fisher's exact test), Q value = 0.0097

Table S248. Gene #25: 'amp_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 25(11P11.2) MUTATED	2	4	0	0	0
AMP PEAK 25(11P11.2) WILD-TYPE	12	5	7	7	16

Figure S248. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S249. Gene #25: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 25(11P11.2) MUTATED	48	0	3	1
AMP PEAK 25(11P11.2) WILD-TYPE	160	178	96	53

Figure S249. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S250. Gene #25: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 25(11P11.2) MUTATED	26	12	6
AMP PEAK 25(11P11.2) WILD-TYPE	128	66	187

Figure S250. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'RPPA_CNMF'

P value = 0.00153 (Fisher's exact test), Q value = 0.002

Table S251. Gene #25: 'amp_11p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 25(11P11.2) MUTATED	2	1	3	12	13	6	6
AMP PEAK 25(11P11.2) WILD-TYPE	37	80	49	44	71	62	47

Figure S251. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00906 (Fisher's exact test), Q value = 0.011

Table S252. Gene #25: 'amp_11p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 25(11P11.2) MUTATED	3	26	10	4
AMP PEAK 25(11P11.2) WILD-TYPE	105	156	83	46

Figure S252. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S253. Gene #25: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 25(11P11.2) MUTATED	43	2	1	6
AMP PEAK 25(11P11.2) WILD-TYPE	145	121	92	127

Figure S253. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S254. Gene #25: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 25(11P11.2) MUTATED	35	1	3	2	6	4	1
AMP PEAK 25(11P11.2) WILD-TYPE	88	52	44	63	102	62	74

Figure S254. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S255. Gene #25: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 25(11P11.2) MUTATED	34	3	3	6	5
AMP PEAK 25(11P11.2) WILD-TYPE	130	77	103	127	42

Figure S255. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S256. Gene #25: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 25(11P11.2) MUTATED	11	36	4
AMP PEAK 25(11P11.2) WILD-TYPE	207	136	136

Figure S256. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.031

Table S257. Gene #25: 'amp_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 25(11P11.2) MUTATED	20	5	9	7
AMP PEAK 25(11P11.2) WILD-TYPE	96	93	83	85

Figure S257. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.023

Table S258. Gene #25: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 25(11P11.2) MUTATED	21	6	14
AMP PEAK 25(11P11.2) WILD-TYPE	142	126	89

Figure S258. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.2' versus 'MRNA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.00079

Table S259. Gene #26: 'amp_11q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 26(11Q13.2) MUTATED	0	7	0	0
AMP PEAK 26(11Q13.2) WILD-TYPE	15	10	14	7

Figure S259. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00943 (Fisher's exact test), Q value = 0.011

Table S260. Gene #26: 'amp_11q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 26(11Q13.2) MUTATED	3	4	0	0	0
AMP PEAK 26(11Q13.2) WILD-TYPE	11	5	7	7	16

Figure S260. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S261. Gene #26: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 26(11Q13.2) MUTATED	65	4	3	2
AMP PEAK 26(11Q13.2) WILD-TYPE	143	174	96	52

Figure S261. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00023

Table S262. Gene #26: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 26(11Q13.2) MUTATED	37	11	15
AMP PEAK 26(11Q13.2) WILD-TYPE	117	67	178

Figure S262. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'RPPA_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0026

Table S263. Gene #26: 'amp_11q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 26(11Q13.2) MUTATED	2	4	8	15	18	7	9
AMP PEAK 26(11Q13.2) WILD-TYPE	37	77	44	41	66	61	44

Figure S263. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.00094

Table S264. Gene #26: 'amp_11q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 26(11Q13.2) MUTATED	5	39	13	6
AMP PEAK 26(11Q13.2) WILD-TYPE	103	143	80	44

Figure S264. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S265. Gene #26: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 26(11Q13.2) MUTATED	51	7	3	12
AMP PEAK 26(11Q13.2) WILD-TYPE	137	116	90	121

Figure S265. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S266. Gene #26: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 26(11Q13.2) MUTATED	39	1	2	2	16	10	3
AMP PEAK 26(11Q13.2) WILD-TYPE	84	52	45	63	92	56	72

Figure S266. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S267. Gene #26: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 26(11Q13.2) MUTATED	44	3	5	15	5
AMP PEAK 26(11Q13.2) WILD-TYPE	120	77	101	118	42

Figure S267. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S268. Gene #26: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 26(11Q13.2) MUTATED	19	41	12
AMP PEAK 26(11Q13.2) WILD-TYPE	199	131	128

Figure S268. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00437 (Fisher's exact test), Q value = 0.0055

Table S269. Gene #26: 'amp_11q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 26(11Q13.2) MUTATED	36	13	10
AMP PEAK 26(11Q13.2) WILD-TYPE	127	119	93

Figure S269. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S270. Gene #27: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 27(11Q14.1) MUTATED	54	2	2	2
AMP PEAK 27(11Q14.1) WILD-TYPE	154	176	97	52

Figure S270. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S271. Gene #27: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 27(11Q14.1) MUTATED	32	9	10
AMP PEAK 27(11Q14.1) WILD-TYPE	122	69	183

Figure S271. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'RPPA_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.029

Table S272. Gene #27: 'amp_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 27(11Q14.1) MUTATED	1	4	6	10	16	6	7
AMP PEAK 27(11Q14.1) WILD-TYPE	38	77	46	46	68	62	46

Figure S272. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00224 (Fisher's exact test), Q value = 0.0029

Table S273. Gene #27: 'amp_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 27(11Q14.1) MUTATED	4	32	10	4
AMP PEAK 27(11Q14.1) WILD-TYPE	104	150	83	46

Figure S273. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S274. Gene #27: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 27(11Q14.1) MUTATED	41	6	4	8
AMP PEAK 27(11Q14.1) WILD-TYPE	147	117	89	125

Figure S274. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S275. Gene #27: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 27(11Q14.1) MUTATED	34	1	4	2	9	7	2
AMP PEAK 27(11Q14.1) WILD-TYPE	89	52	43	63	99	59	73

Figure S275. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S276. Gene #27: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 27(11Q14.1) MUTATED	35	3	4	12	6
AMP PEAK 27(11Q14.1) WILD-TYPE	129	77	102	121	41

Figure S276. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S277. Gene #27: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 27(11Q14.1) MUTATED	13	38	9
AMP PEAK 27(11Q14.1) WILD-TYPE	205	134	131

Figure S277. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.033

Table S278. Gene #27: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 27(11Q14.1) MUTATED	23	7	8	11
AMP PEAK 27(11Q14.1) WILD-TYPE	93	91	84	81

Figure S278. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0263 (Fisher's exact test), Q value = 0.03

Table S279. Gene #27: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 27(11Q14.1) MUTATED	28	9	12
AMP PEAK 27(11Q14.1) WILD-TYPE	135	123	91

Figure S279. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S280. Gene #28: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 28(12P12.1) MUTATED	72	5	7	8
AMP PEAK 28(12P12.1) WILD-TYPE	136	173	92	46

Figure S280. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S281. Gene #28: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 28(12P12.1) MUTATED	48	17	11
AMP PEAK 28(12P12.1) WILD-TYPE	106	61	182

Figure S281. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0013

Table S282. Gene #28: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 28(12P12.1) MUTATED	12	48	11	5
AMP PEAK 28(12P12.1) WILD-TYPE	96	134	82	45

Figure S282. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S283. Gene #28: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 28(12P12.1) MUTATED	61	9	12	10
AMP PEAK 28(12P12.1) WILD-TYPE	127	114	81	123

Figure S283. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S284. Gene #28: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 28(12P12.1) MUTATED	48	2	11	6	13	3	9
AMP PEAK 28(12P12.1) WILD-TYPE	75	51	36	59	95	63	66

Figure S284. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S285. Gene #28: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 28(12P12.1) MUTATED	51	7	13	10	11
AMP PEAK 28(12P12.1) WILD-TYPE	113	73	93	123	36

Figure S285. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S286. Gene #28: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 28(12P12.1) MUTATED	23	57	12
AMP PEAK 28(12P12.1) WILD-TYPE	195	115	128

Figure S286. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.00094

Table S287. Gene #28: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 28(12P12.1) MUTATED	34	8	13	18
AMP PEAK 28(12P12.1) WILD-TYPE	82	90	79	74

Figure S287. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S288. Gene #28: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 28(12P12.1) MUTATED	45	10	18
AMP PEAK 28(12P12.1) WILD-TYPE	118	122	85

Figure S288. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S289. Gene #29: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 29(12Q13.11) MUTATED	71	4	5	7
AMP PEAK 29(12Q13.11) WILD-TYPE	137	174	94	47

Figure S289. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S290. Gene #29: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 29(12Q13.11) MUTATED	43	20	8
AMP PEAK 29(12Q13.11) WILD-TYPE	111	58	185

Figure S290. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.11' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S291. Gene #29: 'amp_12q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 29(12Q13.11) MUTATED	1	6	5	13	27	12	8
AMP PEAK 29(12Q13.11) WILD-TYPE	38	75	47	43	57	56	45

Figure S291. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q13.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.00084

Table S292. Gene #29: 'amp_12q13.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 29(12Q13.11) MUTATED	9	46	12	5
AMP PEAK 29(12Q13.11) WILD-TYPE	99	136	81	45

Figure S292. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q13.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S293. Gene #29: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 29(12Q13.11) MUTATED	57	7	13	9
AMP PEAK 29(12Q13.11) WILD-TYPE	131	116	80	124

Figure S293. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S294. Gene #29: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 29(12Q13.11) MUTATED	45	1	12	6	11	4	7
AMP PEAK 29(12Q13.11) WILD-TYPE	78	52	35	59	97	62	68

Figure S294. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S295. Gene #29: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 29(12Q13.11) MUTATED	51	7	13	9	7
AMP PEAK 29(12Q13.11) WILD-TYPE	113	73	93	124	40

Figure S295. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S296. Gene #29: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 29(12Q13.11) MUTATED	19	57	11
AMP PEAK 29(12Q13.11) WILD-TYPE	199	115	129

Figure S296. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00249 (Fisher's exact test), Q value = 0.0032

Table S297. Gene #29: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 29(12Q13.11) MUTATED	30	7	13	16
AMP PEAK 29(12Q13.11) WILD-TYPE	86	91	79	76

Figure S297. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S298. Gene #29: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 29(12Q13.11) MUTATED	41	9	16
AMP PEAK 29(12Q13.11) WILD-TYPE	122	123	87

Figure S298. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S299. Gene #30: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 30(12Q13.2) MUTATED	83	4	6	7
AMP PEAK 30(12Q13.2) WILD-TYPE	125	174	93	47

Figure S299. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S300. Gene #30: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 30(12Q13.2) MUTATED	48	20	14
AMP PEAK 30(12Q13.2) WILD-TYPE	106	58	179

Figure S300. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.2' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S301. Gene #30: 'amp_12q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 30(12Q13.2) MUTATED	1	8	6	17	26	12	8
AMP PEAK 30(12Q13.2) WILD-TYPE	38	73	46	39	58	56	45

Figure S301. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.00075

Table S302. Gene #30: 'amp_12q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 30(12Q13.2) MUTATED	10	49	14	5
AMP PEAK 30(12Q13.2) WILD-TYPE	98	133	79	45

Figure S302. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S303. Gene #30: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 30(12Q13.2) MUTATED	61	8	17	13
AMP PEAK 30(12Q13.2) WILD-TYPE	127	115	76	120

Figure S303. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S304. Gene #30: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 30(12Q13.2) MUTATED	46	1	16	6	15	7	8
AMP PEAK 30(12Q13.2) WILD-TYPE	77	52	31	59	93	59	67

Figure S304. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S305. Gene #30: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 30(12Q13.2) MUTATED	57	6	15	12	8
AMP PEAK 30(12Q13.2) WILD-TYPE	107	74	91	121	39

Figure S305. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S306. Gene #30: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 30(12Q13.2) MUTATED	20	63	15
AMP PEAK 30(12Q13.2) WILD-TYPE	198	109	125

Figure S306. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00029

Table S307. Gene #30: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 30(12Q13.2) MUTATED	37	10	11	20
AMP PEAK 30(12Q13.2) WILD-TYPE	79	88	81	72

Figure S307. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S308. Gene #30: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 30(12Q13.2) MUTATED	47	13	18
AMP PEAK 30(12Q13.2) WILD-TYPE	116	119	85

Figure S308. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S309. Gene #31: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 31(13Q34) MUTATED	53	1	2	2
AMP PEAK 31(13Q34) WILD-TYPE	155	177	97	52

Figure S309. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S310. Gene #31: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 31(13Q34) MUTATED	34	14	5
AMP PEAK 31(13Q34) WILD-TYPE	120	64	188

Figure S310. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.00084

Table S311. Gene #31: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 31(13Q34) MUTATED	0	2	4	8	18	7	6
AMP PEAK 31(13Q34) WILD-TYPE	39	79	48	48	66	61	47

Figure S311. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S312. Gene #31: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 31(13Q34) MUTATED	1	32	9	3
AMP PEAK 31(13Q34) WILD-TYPE	107	150	84	47

Figure S312. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S313. Gene #31: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 31(13Q34) MUTATED	50	0	5	3
AMP PEAK 31(13Q34) WILD-TYPE	138	123	88	130

Figure S313. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S314. Gene #31: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 31(13Q34) MUTATED	46	0	5	2	3	1	1
AMP PEAK 31(13Q34) WILD-TYPE	77	53	42	63	105	65	74

Figure S314. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S315. Gene #31: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 31(13Q34) MUTATED	42	2	6	3	5
AMP PEAK 31(13Q34) WILD-TYPE	122	78	100	130	42

Figure S315. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S316. Gene #31: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 31(13Q34) MUTATED	8	46	4
AMP PEAK 31(13Q34) WILD-TYPE	210	126	136

Figure S316. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00027

Table S317. Gene #31: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 31(13Q34) MUTATED	24	2	12	14
AMP PEAK 31(13Q34) WILD-TYPE	92	96	80	78

Figure S317. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S318. Gene #31: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 31(13Q34) MUTATED	31	4	17
AMP PEAK 31(13Q34) WILD-TYPE	132	128	86

Figure S318. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.012

Table S319. Gene #32: 'amp_14q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 32(14Q24.3) MUTATED	1	5	0	1	1
AMP PEAK 32(14Q24.3) WILD-TYPE	13	4	7	6	15

Figure S319. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S320. Gene #32: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 32(14Q24.3) MUTATED	56	1	2	5
AMP PEAK 32(14Q24.3) WILD-TYPE	152	177	97	49

Figure S320. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q24.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S321. Gene #32: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 32(14Q24.3) MUTATED	32	12	10
AMP PEAK 32(14Q24.3) WILD-TYPE	122	66	183

Figure S321. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q24.3' versus 'RPPA_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0023

Table S322. Gene #32: 'amp_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 32(14Q24.3) MUTATED	3	4	1	9	13	4	12
AMP PEAK 32(14Q24.3) WILD-TYPE	36	77	51	47	71	64	41

Figure S322. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.014

Table S323. Gene #32: 'amp_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 32(14Q24.3) MUTATED	4	28	8	6
AMP PEAK 32(14Q24.3) WILD-TYPE	104	154	85	44

Figure S323. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S324. Gene #32: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 32(14Q24.3) MUTATED	52	4	1	7
AMP PEAK 32(14Q24.3) WILD-TYPE	136	119	92	126

Figure S324. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S325. Gene #32: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 32(14Q24.3) MUTATED	40	1	8	1	9	1	4
AMP PEAK 32(14Q24.3) WILD-TYPE	83	52	39	64	99	65	71

Figure S325. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S326. Gene #32: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 32(14Q24.3) MUTATED	38	5	3	9	7
AMP PEAK 32(14Q24.3) WILD-TYPE	126	75	103	124	40

Figure S326. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S327. Gene #32: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 32(14Q24.3) MUTATED	11	42	9
AMP PEAK 32(14Q24.3) WILD-TYPE	207	130	131

Figure S327. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.052

Table S328. Gene #32: 'amp_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 32(14Q24.3) MUTATED	23	7	10	13
AMP PEAK 32(14Q24.3) WILD-TYPE	93	91	82	79

Figure S328. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.018

Table S329. Gene #32: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 32(14Q24.3) MUTATED	25	9	19
AMP PEAK 32(14Q24.3) WILD-TYPE	138	123	84

Figure S329. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S330. Gene #33: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 33(14Q32.33) MUTATED	71	1	2	5
AMP PEAK 33(14Q32.33) WILD-TYPE	137	177	97	49

Figure S330. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q32.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S331. Gene #33: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 33(14Q32.33) MUTATED	42	13	13
AMP PEAK 33(14Q32.33) WILD-TYPE	112	65	180

Figure S331. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'RPPA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00031

Table S332. Gene #33: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 33(14Q32.33) MUTATED	3	5	4	16	19	4	10
AMP PEAK 33(14Q32.33) WILD-TYPE	36	76	48	40	65	64	43

Figure S332. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q32.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.00065

Table S333. Gene #33: 'amp_14q32.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 33(14Q32.33) MUTATED	4	37	15	5
AMP PEAK 33(14Q32.33) WILD-TYPE	104	145	78	45

Figure S333. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S334. Gene #33: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 33(14Q32.33) MUTATED	58	5	3	12
AMP PEAK 33(14Q32.33) WILD-TYPE	130	118	90	121

Figure S334. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S335. Gene #33: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 33(14Q32.33) MUTATED	38	1	12	3	13	7	4
AMP PEAK 33(14Q32.33) WILD-TYPE	85	52	35	62	95	59	71

Figure S335. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S336. Gene #33: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 33(14Q32.33) MUTATED	47	7	6	13	5
AMP PEAK 33(14Q32.33) WILD-TYPE	117	73	100	120	42

Figure S336. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q32.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S337. Gene #33: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 33(14Q32.33) MUTATED	15	52	11
AMP PEAK 33(14Q32.33) WILD-TYPE	203	120	129

Figure S337. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.0062

Table S338. Gene #33: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 33(14Q32.33) MUTATED	31	10	10	16
AMP PEAK 33(14Q32.33) WILD-TYPE	85	88	82	76

Figure S338. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0318 (Fisher's exact test), Q value = 0.036

Table S339. Gene #33: 'amp_14q32.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 33(14Q32.33) MUTATED	36	14	17
AMP PEAK 33(14Q32.33) WILD-TYPE	127	118	86

Figure S339. Get High-res Image Gene #33: 'amp_14q32.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S340. Gene #34: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 34(15Q26.3) MUTATED	35	2	0	1
AMP PEAK 34(15Q26.3) WILD-TYPE	173	176	99	53

Figure S340. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.005

Table S341. Gene #34: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 34(15Q26.3) MUTATED	20	8	7
AMP PEAK 34(15Q26.3) WILD-TYPE	134	70	186

Figure S341. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'RPPA_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.053

Table S342. Gene #34: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 34(15Q26.3) MUTATED	0	1	2	5	8	5	6
AMP PEAK 34(15Q26.3) WILD-TYPE	39	80	50	51	76	63	47

Figure S342. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S343. Gene #34: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 34(15Q26.3) MUTATED	29	2	4	3
AMP PEAK 34(15Q26.3) WILD-TYPE	159	121	89	130

Figure S343. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S344. Gene #34: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 34(15Q26.3) MUTATED	20	1	6	1	8	2	0
AMP PEAK 34(15Q26.3) WILD-TYPE	103	52	41	64	100	64	75

Figure S344. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S345. Gene #34: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 34(15Q26.3) MUTATED	25	2	6	2	3
AMP PEAK 34(15Q26.3) WILD-TYPE	139	78	100	131	44

Figure S345. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S346. Gene #34: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 34(15Q26.3) MUTATED	8	27	3
AMP PEAK 34(15Q26.3) WILD-TYPE	210	145	137

Figure S346. Get High-res Image Gene #34: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.01

Table S347. Gene #35: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 35(16P11.2) MUTATED	0	5	0	0
AMP PEAK 35(16P11.2) WILD-TYPE	15	12	14	7

Figure S347. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.0064

Table S348. Gene #35: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 35(16P11.2) MUTATED	1	4	0	0	0
AMP PEAK 35(16P11.2) WILD-TYPE	13	5	7	7	16

Figure S348. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S349. Gene #35: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 35(16P11.2) MUTATED	62	0	1	3
AMP PEAK 35(16P11.2) WILD-TYPE	146	178	98	51

Figure S349. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S350. Gene #35: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 35(16P11.2) MUTATED	34	15	8
AMP PEAK 35(16P11.2) WILD-TYPE	120	63	185

Figure S350. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CNMF'

P value = 0.00238 (Fisher's exact test), Q value = 0.0031

Table S351. Gene #35: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 35(16P11.2) MUTATED	1	2	7	10	16	10	9
AMP PEAK 35(16P11.2) WILD-TYPE	38	79	45	46	68	58	44

Figure S351. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_16p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00038

Table S352. Gene #35: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 35(16P11.2) MUTATED	3	35	12	5
AMP PEAK 35(16P11.2) WILD-TYPE	105	147	81	45

Figure S352. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S353. Gene #35: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 35(16P11.2) MUTATED	54	4	5	3
AMP PEAK 35(16P11.2) WILD-TYPE	134	119	88	130

Figure S353. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S354. Gene #35: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 35(16P11.2) MUTATED	46	3	4	1	9	3	0
AMP PEAK 35(16P11.2) WILD-TYPE	77	50	43	64	99	63	75

Figure S354. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S355. Gene #35: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 35(16P11.2) MUTATED	45	3	5	4	6
AMP PEAK 35(16P11.2) WILD-TYPE	119	77	101	129	41

Figure S355. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S356. Gene #35: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 35(16P11.2) MUTATED	13	46	4
AMP PEAK 35(16P11.2) WILD-TYPE	205	126	136

Figure S356. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0011

Table S357. Gene #35: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 35(16P11.2) MUTATED	26	4	10	12
AMP PEAK 35(16P11.2) WILD-TYPE	90	94	82	80

Figure S357. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00303 (Fisher's exact test), Q value = 0.0039

Table S358. Gene #35: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 35(16P11.2) MUTATED	27	7	18
AMP PEAK 35(16P11.2) WILD-TYPE	136	125	85

Figure S358. Get High-res Image Gene #35: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S359. Gene #36: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 36(17Q11.2) MUTATED	64	3	1	3
AMP PEAK 36(17Q11.2) WILD-TYPE	144	175	98	51

Figure S359. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S360. Gene #36: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 36(17Q11.2) MUTATED	46	13	4
AMP PEAK 36(17Q11.2) WILD-TYPE	108	65	189

Figure S360. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S361. Gene #36: 'amp_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 36(17Q11.2) MUTATED	2	0	2	15	22	10	5
AMP PEAK 36(17Q11.2) WILD-TYPE	37	81	50	41	62	58	48

Figure S361. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S362. Gene #36: 'amp_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 36(17Q11.2) MUTATED	3	36	15	2
AMP PEAK 36(17Q11.2) WILD-TYPE	105	146	78	48

Figure S362. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S363. Gene #36: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 36(17Q11.2) MUTATED	61	1	5	3
AMP PEAK 36(17Q11.2) WILD-TYPE	127	122	88	130

Figure S363. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S364. Gene #36: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 36(17Q11.2) MUTATED	50	0	9	2	6	3	0
AMP PEAK 36(17Q11.2) WILD-TYPE	73	53	38	63	102	63	75

Figure S364. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S365. Gene #36: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 36(17Q11.2) MUTATED	55	2	6	2	3
AMP PEAK 36(17Q11.2) WILD-TYPE	109	78	100	131	44

Figure S365. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S366. Gene #36: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 36(17Q11.2) MUTATED	12	54	2
AMP PEAK 36(17Q11.2) WILD-TYPE	206	118	138

Figure S366. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S367. Gene #36: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 36(17Q11.2) MUTATED	31	5	11	11
AMP PEAK 36(17Q11.2) WILD-TYPE	85	93	81	81

Figure S367. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S368. Gene #36: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 36(17Q11.2) MUTATED	39	5	14
AMP PEAK 36(17Q11.2) WILD-TYPE	124	127	89

Figure S368. Get High-res Image Gene #36: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00225 (Fisher's exact test), Q value = 0.0029

Table S369. Gene #37: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 37(17Q12) MUTATED	0	4	1	0	0
AMP PEAK 37(17Q12) WILD-TYPE	14	5	6	7	16

Figure S369. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S370. Gene #37: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 37(17Q12) MUTATED	67	4	3	1
AMP PEAK 37(17Q12) WILD-TYPE	141	174	96	53

Figure S370. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S371. Gene #37: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 37(17Q12) MUTATED	47	14	2
AMP PEAK 37(17Q12) WILD-TYPE	107	64	191

Figure S371. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S372. Gene #37: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 37(17Q12) MUTATED	1	2	1	10	28	9	9
AMP PEAK 37(17Q12) WILD-TYPE	38	79	51	46	56	59	44

Figure S372. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S373. Gene #37: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 37(17Q12) MUTATED	4	43	7	6
AMP PEAK 37(17Q12) WILD-TYPE	104	139	86	44

Figure S373. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S374. Gene #37: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 37(17Q12) MUTATED	61	1	11	2
AMP PEAK 37(17Q12) WILD-TYPE	127	122	82	131

Figure S374. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S375. Gene #37: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 37(17Q12) MUTATED	51	0	15	2	5	2	0
AMP PEAK 37(17Q12) WILD-TYPE	72	53	32	63	103	64	75

Figure S375. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S376. Gene #37: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 37(17Q12) MUTATED	58	1	9	3	2
AMP PEAK 37(17Q12) WILD-TYPE	106	79	97	130	45

Figure S376. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S377. Gene #37: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 37(17Q12) MUTATED	7	63	3
AMP PEAK 37(17Q12) WILD-TYPE	211	109	137

Figure S377. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00034

Table S378. Gene #37: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 37(17Q12) MUTATED	30	5	11	14
AMP PEAK 37(17Q12) WILD-TYPE	86	93	81	78

Figure S378. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S379. Gene #37: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 37(17Q12) MUTATED	38	4	18
AMP PEAK 37(17Q12) WILD-TYPE	125	128	85

Figure S379. Get High-res Image Gene #37: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S380. Gene #38: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 38(17Q25.1) MUTATED	0	10	1	0
AMP PEAK 38(17Q25.1) WILD-TYPE	15	7	13	7

Figure S380. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S381. Gene #38: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 38(17Q25.1) MUTATED	2	8	1	0	0
AMP PEAK 38(17Q25.1) WILD-TYPE	12	1	6	7	16

Figure S381. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S382. Gene #38: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 38(17Q25.1) MUTATED	95	4	3	3
AMP PEAK 38(17Q25.1) WILD-TYPE	113	174	96	51

Figure S382. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S383. Gene #38: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 38(17Q25.1) MUTATED	54	23	8
AMP PEAK 38(17Q25.1) WILD-TYPE	100	55	185

Figure S383. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S384. Gene #38: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 38(17Q25.1) MUTATED	3	1	5	14	38	11	13
AMP PEAK 38(17Q25.1) WILD-TYPE	36	80	47	42	46	57	40

Figure S384. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S385. Gene #38: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 38(17Q25.1) MUTATED	4	56	18	7
AMP PEAK 38(17Q25.1) WILD-TYPE	104	126	75	43

Figure S385. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S386. Gene #38: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 38(17Q25.1) MUTATED	81	5	11	7
AMP PEAK 38(17Q25.1) WILD-TYPE	107	118	82	126

Figure S386. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S387. Gene #38: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 38(17Q25.1) MUTATED	72	0	13	2	9	7	1
AMP PEAK 38(17Q25.1) WILD-TYPE	51	53	34	63	99	59	74

Figure S387. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S388. Gene #38: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 38(17Q25.1) MUTATED	77	5	9	7	3
AMP PEAK 38(17Q25.1) WILD-TYPE	87	75	97	126	44

Figure S388. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S389. Gene #38: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 38(17Q25.1) MUTATED	18	77	6
AMP PEAK 38(17Q25.1) WILD-TYPE	200	95	134

Figure S389. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S390. Gene #38: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 38(17Q25.1) MUTATED	42	7	19	13
AMP PEAK 38(17Q25.1) WILD-TYPE	74	91	73	79

Figure S390. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S391. Gene #38: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 38(17Q25.1) MUTATED	43	10	28
AMP PEAK 38(17Q25.1) WILD-TYPE	120	122	75

Figure S391. Get High-res Image Gene #38: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S392. Gene #39: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 39(18P11.31) MUTATED	90	1	3	2
AMP PEAK 39(18P11.31) WILD-TYPE	118	177	96	52

Figure S392. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S393. Gene #39: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 39(18P11.31) MUTATED	55	22	8
AMP PEAK 39(18P11.31) WILD-TYPE	99	56	185

Figure S393. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S394. Gene #39: 'amp_18p11.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 39(18P11.31) MUTATED	1	1	5	20	25	13	10
AMP PEAK 39(18P11.31) WILD-TYPE	38	80	47	36	59	55	43

Figure S394. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18p11.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S395. Gene #39: 'amp_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 39(18P11.31) MUTATED	4	50	15	6
AMP PEAK 39(18P11.31) WILD-TYPE	104	132	78	44

Figure S395. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S396. Gene #39: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 39(18P11.31) MUTATED	77	2	9	8
AMP PEAK 39(18P11.31) WILD-TYPE	111	121	84	125

Figure S396. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S397. Gene #39: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 39(18P11.31) MUTATED	61	1	17	1	9	4	3
AMP PEAK 39(18P11.31) WILD-TYPE	62	52	30	64	99	62	72

Figure S397. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S398. Gene #39: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 39(18P11.31) MUTATED	69	5	6	6	9
AMP PEAK 39(18P11.31) WILD-TYPE	95	75	100	127	38

Figure S398. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S399. Gene #39: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 39(18P11.31) MUTATED	15	74	6
AMP PEAK 39(18P11.31) WILD-TYPE	203	98	134

Figure S399. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S400. Gene #39: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 39(18P11.31) MUTATED	38	7	22	15
AMP PEAK 39(18P11.31) WILD-TYPE	78	91	70	77

Figure S400. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S401. Gene #39: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 39(18P11.31) MUTATED	45	8	29
AMP PEAK 39(18P11.31) WILD-TYPE	118	124	74

Figure S401. Get High-res Image Gene #39: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S402. Gene #40: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 40(18Q11.2) MUTATED	63	1	2	3
AMP PEAK 40(18Q11.2) WILD-TYPE	145	177	97	51

Figure S402. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S403. Gene #40: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 40(18Q11.2) MUTATED	39	18	4
AMP PEAK 40(18Q11.2) WILD-TYPE	115	60	189

Figure S403. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S404. Gene #40: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 40(18Q11.2) MUTATED	1	1	3	15	20	10	6
AMP PEAK 40(18Q11.2) WILD-TYPE	38	80	49	41	64	58	47

Figure S404. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S405. Gene #40: 'amp_18q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 40(18Q11.2) MUTATED	1	39	13	3
AMP PEAK 40(18Q11.2) WILD-TYPE	107	143	80	47

Figure S405. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S406. Gene #40: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 40(18Q11.2) MUTATED	59	2	5	3
AMP PEAK 40(18Q11.2) WILD-TYPE	129	121	88	130

Figure S406. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S407. Gene #40: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 40(18Q11.2) MUTATED	49	1	9	1	6	2	1
AMP PEAK 40(18Q11.2) WILD-TYPE	74	52	38	64	102	64	74

Figure S407. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S408. Gene #40: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 40(18Q11.2) MUTATED	53	5	4	1	5
AMP PEAK 40(18Q11.2) WILD-TYPE	111	75	102	132	42

Figure S408. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S409. Gene #40: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 40(18Q11.2) MUTATED	13	54	1
AMP PEAK 40(18Q11.2) WILD-TYPE	205	118	139

Figure S409. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S410. Gene #40: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 40(18Q11.2) MUTATED	31	2	12	12
AMP PEAK 40(18Q11.2) WILD-TYPE	85	96	80	80

Figure S410. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S411. Gene #40: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 40(18Q11.2) MUTATED	37	1	19
AMP PEAK 40(18Q11.2) WILD-TYPE	126	131	84

Figure S411. Get High-res Image Gene #40: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S412. Gene #41: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 41(19P13.2) MUTATED	0	9	0	0
AMP PEAK 41(19P13.2) WILD-TYPE	15	8	14	7

Figure S412. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S413. Gene #41: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 41(19P13.2) MUTATED	2	7	0	0	0
AMP PEAK 41(19P13.2) WILD-TYPE	12	2	7	7	16

Figure S413. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S414. Gene #41: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 41(19P13.2) MUTATED	89	0	1	2
AMP PEAK 41(19P13.2) WILD-TYPE	119	178	98	52

Figure S414. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S415. Gene #41: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 41(19P13.2) MUTATED	44	28	9
AMP PEAK 41(19P13.2) WILD-TYPE	110	50	184

Figure S415. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S416. Gene #41: 'amp_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 41(19P13.2) MUTATED	1	3	4	16	26	10	10
AMP PEAK 41(19P13.2) WILD-TYPE	38	78	48	40	58	58	43

Figure S416. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S417. Gene #41: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 41(19P13.2) MUTATED	3	52	9	6
AMP PEAK 41(19P13.2) WILD-TYPE	105	130	84	44

Figure S417. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S418. Gene #41: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 41(19P13.2) MUTATED	78	3	3	7
AMP PEAK 41(19P13.2) WILD-TYPE	110	120	90	126

Figure S418. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S419. Gene #41: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 41(19P13.2) MUTATED	68	1	4	2	9	6	1
AMP PEAK 41(19P13.2) WILD-TYPE	55	52	43	63	99	60	74

Figure S419. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S420. Gene #41: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 41(19P13.2) MUTATED	67	4	4	8	6
AMP PEAK 41(19P13.2) WILD-TYPE	97	76	102	125	41

Figure S420. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S421. Gene #41: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 41(19P13.2) MUTATED	19	62	8
AMP PEAK 41(19P13.2) WILD-TYPE	199	110	132

Figure S421. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S422. Gene #41: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 41(19P13.2) MUTATED	40	7	17	11
AMP PEAK 41(19P13.2) WILD-TYPE	76	91	75	81

Figure S422. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00664 (Fisher's exact test), Q value = 0.0082

Table S423. Gene #41: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 41(19P13.2) MUTATED	40	14	21
AMP PEAK 41(19P13.2) WILD-TYPE	123	118	82

Figure S423. Get High-res Image Gene #41: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.0045

Table S424. Gene #42: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 42(19P13.12) MUTATED	1	7	0	0
AMP PEAK 42(19P13.12) WILD-TYPE	14	10	14	7

Figure S424. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00025

Table S425. Gene #42: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 42(19P13.12) MUTATED	2	6	0	0	0
AMP PEAK 42(19P13.12) WILD-TYPE	12	3	7	7	16

Figure S425. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S426. Gene #42: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 42(19P13.12) MUTATED	96	0	2	1
AMP PEAK 42(19P13.12) WILD-TYPE	112	178	97	53

Figure S426. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S427. Gene #42: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 42(19P13.12) MUTATED	50	27	9
AMP PEAK 42(19P13.12) WILD-TYPE	104	51	184

Figure S427. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S428. Gene #42: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 42(19P13.12) MUTATED	1	3	7	18	25	10	11
AMP PEAK 42(19P13.12) WILD-TYPE	38	78	45	38	59	58	42

Figure S428. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S429. Gene #42: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 42(19P13.12) MUTATED	3	55	11	6
AMP PEAK 42(19P13.12) WILD-TYPE	105	127	82	44

Figure S429. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S430. Gene #42: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 42(19P13.12) MUTATED	85	5	3	5
AMP PEAK 42(19P13.12) WILD-TYPE	103	118	90	128

Figure S430. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S431. Gene #42: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 42(19P13.12) MUTATED	74	2	5	3	9	4	1
AMP PEAK 42(19P13.12) WILD-TYPE	49	51	42	62	99	62	74

Figure S431. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S432. Gene #42: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 42(19P13.12) MUTATED	73	5	6	7	6
AMP PEAK 42(19P13.12) WILD-TYPE	91	75	100	126	41

Figure S432. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S433. Gene #42: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 42(19P13.12) MUTATED	21	69	7
AMP PEAK 42(19P13.12) WILD-TYPE	197	103	133

Figure S433. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S434. Gene #42: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 42(19P13.12) MUTATED	45	6	19	11
AMP PEAK 42(19P13.12) WILD-TYPE	71	92	73	81

Figure S434. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S435. Gene #42: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 42(19P13.12) MUTATED	45	11	25
AMP PEAK 42(19P13.12) WILD-TYPE	118	121	78

Figure S435. Get High-res Image Gene #42: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.00666 (Fisher's exact test), Q value = 0.0082

Table S436. Gene #43: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 43(19Q12) MUTATED	1	8	1	0
AMP PEAK 43(19Q12) WILD-TYPE	14	9	13	7

Figure S436. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S437. Gene #43: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 43(19Q12) MUTATED	2	7	1	0	0
AMP PEAK 43(19Q12) WILD-TYPE	12	2	6	7	16

Figure S437. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S438. Gene #43: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 43(19Q12) MUTATED	118	0	2	1
AMP PEAK 43(19Q12) WILD-TYPE	90	178	97	53

Figure S438. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S439. Gene #43: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 43(19Q12) MUTATED	68	28	11
AMP PEAK 43(19Q12) WILD-TYPE	86	50	182

Figure S439. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S440. Gene #43: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 43(19Q12) MUTATED	1	3	6	18	34	17	13
AMP PEAK 43(19Q12) WILD-TYPE	38	78	46	38	50	51	40

Figure S440. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S441. Gene #43: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 43(19Q12) MUTATED	3	63	19	7
AMP PEAK 43(19Q12) WILD-TYPE	105	119	74	43

Figure S441. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S442. Gene #43: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 43(19Q12) MUTATED	100	3	11	7
AMP PEAK 43(19Q12) WILD-TYPE	88	120	82	126

Figure S442. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S443. Gene #43: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 43(19Q12) MUTATED	81	1	19	3	11	5	1
AMP PEAK 43(19Q12) WILD-TYPE	42	52	28	62	97	61	74

Figure S443. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S444. Gene #43: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 43(19Q12) MUTATED	87	4	10	7	9
AMP PEAK 43(19Q12) WILD-TYPE	77	76	96	126	38

Figure S444. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S445. Gene #43: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 43(19Q12) MUTATED	22	88	7
AMP PEAK 43(19Q12) WILD-TYPE	196	84	133

Figure S445. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S446. Gene #43: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 43(19Q12) MUTATED	50	7	24	20
AMP PEAK 43(19Q12) WILD-TYPE	66	91	68	72

Figure S446. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S447. Gene #43: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 43(19Q12) MUTATED	56	14	31
AMP PEAK 43(19Q12) WILD-TYPE	107	118	72

Figure S447. Get High-res Image Gene #43: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.056

Table S448. Gene #44: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 44(20P13) MUTATED	2	3	0	0	0
AMP PEAK 44(20P13) WILD-TYPE	12	6	7	7	16

Figure S448. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S449. Gene #44: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 44(20P13) MUTATED	104	4	3	6
AMP PEAK 44(20P13) WILD-TYPE	104	174	96	48

Figure S449. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S450. Gene #44: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 44(20P13) MUTATED	65	24	18
AMP PEAK 44(20P13) WILD-TYPE	89	54	175

Figure S450. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p13' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S451. Gene #44: 'amp_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 44(20P13) MUTATED	2	9	5	16	29	16	11
AMP PEAK 44(20P13) WILD-TYPE	37	72	47	40	55	52	42

Figure S451. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S452. Gene #44: 'amp_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 44(20P13) MUTATED	8	54	17	9
AMP PEAK 44(20P13) WILD-TYPE	100	128	76	41

Figure S452. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S453. Gene #44: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 44(20P13) MUTATED	80	10	12	14
AMP PEAK 44(20P13) WILD-TYPE	108	113	81	119

Figure S453. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S454. Gene #44: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 44(20P13) MUTATED	64	5	16	3	12	14	2
AMP PEAK 44(20P13) WILD-TYPE	59	48	31	62	96	52	73

Figure S454. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S455. Gene #44: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 44(20P13) MUTATED	75	8	9	13	11
AMP PEAK 44(20P13) WILD-TYPE	89	72	97	120	36

Figure S455. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S456. Gene #44: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 44(20P13) MUTATED	30	74	12
AMP PEAK 44(20P13) WILD-TYPE	188	98	128

Figure S456. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0038

Table S457. Gene #44: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 44(20P13) MUTATED	40	13	20	25
AMP PEAK 44(20P13) WILD-TYPE	76	85	72	67

Figure S457. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S458. Gene #44: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 44(20P13) MUTATED	57	17	24
AMP PEAK 44(20P13) WILD-TYPE	106	115	79

Figure S458. Get High-res Image Gene #44: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0013

Table S459. Gene #45: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 45(20Q11.21) MUTATED	2	9	0	0
AMP PEAK 45(20Q11.21) WILD-TYPE	13	8	14	7

Figure S459. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S460. Gene #45: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 45(20Q11.21) MUTATED	4	7	0	0	0
AMP PEAK 45(20Q11.21) WILD-TYPE	10	2	7	7	16

Figure S460. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S461. Gene #45: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 45(20Q11.21) MUTATED	139	3	3	7
AMP PEAK 45(20Q11.21) WILD-TYPE	69	175	96	47

Figure S461. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S462. Gene #45: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 45(20Q11.21) MUTATED	79	27	27
AMP PEAK 45(20Q11.21) WILD-TYPE	75	51	166

Figure S462. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S463. Gene #45: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 45(20Q11.21) MUTATED	1	8	7	29	38	19	15
AMP PEAK 45(20Q11.21) WILD-TYPE	38	73	45	27	46	49	38

Figure S463. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S464. Gene #45: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 45(20Q11.21) MUTATED	9	76	23	9
AMP PEAK 45(20Q11.21) WILD-TYPE	99	106	70	41

Figure S464. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S465. Gene #45: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 45(20Q11.21) MUTATED	105	9	17	20
AMP PEAK 45(20Q11.21) WILD-TYPE	83	114	76	113

Figure S465. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S466. Gene #45: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 45(20Q11.21) MUTATED	80	4	21	4	21	17	4
AMP PEAK 45(20Q11.21) WILD-TYPE	43	49	26	61	87	49	71

Figure S466. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S467. Gene #45: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 45(20Q11.21) MUTATED	95	8	15	19	11
AMP PEAK 45(20Q11.21) WILD-TYPE	69	72	91	114	36

Figure S467. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S468. Gene #45: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 45(20Q11.21) MUTATED	32	96	20
AMP PEAK 45(20Q11.21) WILD-TYPE	186	76	120

Figure S468. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S469. Gene #45: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 45(20Q11.21) MUTATED	56	18	23	28
AMP PEAK 45(20Q11.21) WILD-TYPE	60	80	69	64

Figure S469. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S470. Gene #45: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 45(20Q11.21) MUTATED	69	26	30
AMP PEAK 45(20Q11.21) WILD-TYPE	94	106	73

Figure S470. Get High-res Image Gene #45: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.013

Table S471. Gene #46: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 46(20Q13.12) MUTATED	1	6	0	0
AMP PEAK 46(20Q13.12) WILD-TYPE	14	11	14	7

Figure S471. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00939 (Fisher's exact test), Q value = 0.011

Table S472. Gene #46: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 46(20Q13.12) MUTATED	3	4	0	0	0
AMP PEAK 46(20Q13.12) WILD-TYPE	11	5	7	7	16

Figure S472. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S473. Gene #46: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 46(20Q13.12) MUTATED	138	4	3	7
AMP PEAK 46(20Q13.12) WILD-TYPE	70	174	96	47

Figure S473. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S474. Gene #46: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 46(20Q13.12) MUTATED	83	28	27
AMP PEAK 46(20Q13.12) WILD-TYPE	71	50	166

Figure S474. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S475. Gene #46: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 46(20Q13.12) MUTATED	3	7	7	25	38	18	15
AMP PEAK 46(20Q13.12) WILD-TYPE	36	74	45	31	46	50	38

Figure S475. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S476. Gene #46: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 46(20Q13.12) MUTATED	10	73	21	9
AMP PEAK 46(20Q13.12) WILD-TYPE	98	109	72	41

Figure S476. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S477. Gene #46: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 46(20Q13.12) MUTATED	106	10	16	19
AMP PEAK 46(20Q13.12) WILD-TYPE	82	113	77	114

Figure S477. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S478. Gene #46: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 46(20Q13.12) MUTATED	82	4	21	4	21	15	4
AMP PEAK 46(20Q13.12) WILD-TYPE	41	49	26	61	87	51	71

Figure S478. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S479. Gene #46: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 46(20Q13.12) MUTATED	98	8	13	20	12
AMP PEAK 46(20Q13.12) WILD-TYPE	66	72	93	113	35

Figure S479. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S480. Gene #46: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 46(20Q13.12) MUTATED	35	97	19
AMP PEAK 46(20Q13.12) WILD-TYPE	183	75	121

Figure S480. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S481. Gene #46: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 46(20Q13.12) MUTATED	54	18	25	32
AMP PEAK 46(20Q13.12) WILD-TYPE	62	80	67	60

Figure S481. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S482. Gene #46: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 46(20Q13.12) MUTATED	75	24	30
AMP PEAK 46(20Q13.12) WILD-TYPE	88	108	73

Figure S482. Get High-res Image Gene #46: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.013

Table S483. Gene #47: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
AMP PEAK 47(20Q13.33) MUTATED	2	7	0	0
AMP PEAK 47(20Q13.33) WILD-TYPE	13	10	14	7

Figure S483. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0018

Table S484. Gene #47: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 47(20Q13.33) MUTATED	4	5	0	0	0
AMP PEAK 47(20Q13.33) WILD-TYPE	10	4	7	7	16

Figure S484. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S485. Gene #47: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 47(20Q13.33) MUTATED	140	4	3	6
AMP PEAK 47(20Q13.33) WILD-TYPE	68	174	96	48

Figure S485. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S486. Gene #47: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 47(20Q13.33) MUTATED	82	27	27
AMP PEAK 47(20Q13.33) WILD-TYPE	72	51	166

Figure S486. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S487. Gene #47: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 47(20Q13.33) MUTATED	4	9	10	23	40	17	13
AMP PEAK 47(20Q13.33) WILD-TYPE	35	72	42	33	44	51	40

Figure S487. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S488. Gene #47: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 47(20Q13.33) MUTATED	11	78	19	8
AMP PEAK 47(20Q13.33) WILD-TYPE	97	104	74	42

Figure S488. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S489. Gene #47: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 47(20Q13.33) MUTATED	104	13	17	19
AMP PEAK 47(20Q13.33) WILD-TYPE	84	110	76	114

Figure S489. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S490. Gene #47: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 47(20Q13.33) MUTATED	78	4	24	5	22	16	4
AMP PEAK 47(20Q13.33) WILD-TYPE	45	49	23	60	86	50	71

Figure S490. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S491. Gene #47: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 47(20Q13.33) MUTATED	97	9	13	20	11
AMP PEAK 47(20Q13.33) WILD-TYPE	67	71	93	113	36

Figure S491. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S492. Gene #47: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 47(20Q13.33) MUTATED	37	94	19
AMP PEAK 47(20Q13.33) WILD-TYPE	181	78	121

Figure S492. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00033

Table S493. Gene #47: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 47(20Q13.33) MUTATED	53	17	25	32
AMP PEAK 47(20Q13.33) WILD-TYPE	63	81	67	60

Figure S493. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S494. Gene #47: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 47(20Q13.33) MUTATED	72	23	32
AMP PEAK 47(20Q13.33) WILD-TYPE	91	109	71

Figure S494. Get High-res Image Gene #47: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S495. Gene #48: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 48(22Q12.2) MUTATED	57	0	2	3
AMP PEAK 48(22Q12.2) WILD-TYPE	151	178	97	51

Figure S495. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S496. Gene #48: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 48(22Q12.2) MUTATED	40	16	1
AMP PEAK 48(22Q12.2) WILD-TYPE	114	62	192

Figure S496. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S497. Gene #48: 'amp_22q12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
AMP PEAK 48(22Q12.2) MUTATED	0	0	2	12	24	6	8
AMP PEAK 48(22Q12.2) WILD-TYPE	39	81	50	44	60	62	45

Figure S497. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S498. Gene #48: 'amp_22q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 48(22Q12.2) MUTATED	1	41	6	4
AMP PEAK 48(22Q12.2) WILD-TYPE	107	141	87	46

Figure S498. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S499. Gene #48: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 48(22Q12.2) MUTATED	54	1	6	0
AMP PEAK 48(22Q12.2) WILD-TYPE	134	122	87	133

Figure S499. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S500. Gene #48: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 48(22Q12.2) MUTATED	43	1	15	0	2	0	0
AMP PEAK 48(22Q12.2) WILD-TYPE	80	52	32	65	106	66	75

Figure S500. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S501. Gene #48: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 48(22Q12.2) MUTATED	47	1	9	0	4
AMP PEAK 48(22Q12.2) WILD-TYPE	117	79	97	133	43

Figure S501. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S502. Gene #48: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 48(22Q12.2) MUTATED	3	58	0
AMP PEAK 48(22Q12.2) WILD-TYPE	215	114	140

Figure S502. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S503. Gene #48: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 48(22Q12.2) MUTATED	29	1	6	20
AMP PEAK 48(22Q12.2) WILD-TYPE	87	97	86	72

Figure S503. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S504. Gene #48: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 48(22Q12.2) MUTATED	40	2	14
AMP PEAK 48(22Q12.2) WILD-TYPE	123	130	89

Figure S504. Get High-res Image Gene #48: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S505. Gene #49: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 49(XP11.23) MUTATED	61	2	20	7
AMP PEAK 49(XP11.23) WILD-TYPE	147	176	79	47

Figure S505. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0017

Table S506. Gene #49: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
AMP PEAK 49(XP11.23) MUTATED	32	20	19
AMP PEAK 49(XP11.23) WILD-TYPE	122	58	174

Figure S506. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S507. Gene #49: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 49(XP11.23) MUTATED	52	14	9	15
AMP PEAK 49(XP11.23) WILD-TYPE	136	109	84	118

Figure S507. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.00063

Table S508. Gene #49: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 49(XP11.23) MUTATED	38	5	10	6	14	9	8
AMP PEAK 49(XP11.23) WILD-TYPE	85	48	37	59	94	57	67

Figure S508. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.0075

Table S509. Gene #49: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 49(XP11.23) MUTATED	43	11	12	16	7
AMP PEAK 49(XP11.23) WILD-TYPE	121	69	94	117	40

Figure S509. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.00069

Table S510. Gene #49: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 49(XP11.23) MUTATED	28	45	16
AMP PEAK 49(XP11.23) WILD-TYPE	190	127	124

Figure S510. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.003

Table S511. Gene #49: 'amp_xp11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 49(XP11.23) MUTATED	33	10	12	13
AMP PEAK 49(XP11.23) WILD-TYPE	83	88	80	79

Figure S511. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00787 (Fisher's exact test), Q value = 0.0096

Table S512. Gene #49: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
AMP PEAK 49(XP11.23) MUTATED	35	12	21
AMP PEAK 49(XP11.23) WILD-TYPE	128	120	82

Figure S512. Get High-res Image Gene #49: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'MRNA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.031

Table S513. Gene #50: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 50(XQ28) MUTATED	1	5	1	1	1
AMP PEAK 50(XQ28) WILD-TYPE	13	4	6	6	15

Figure S513. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S514. Gene #50: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
AMP PEAK 50(XQ28) MUTATED	63	3	21	6
AMP PEAK 50(XQ28) WILD-TYPE	145	175	78	48

Figure S514. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.044

Table S515. Gene #50: 'amp_xq28' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 50(XQ28) MUTATED	16	45	14	5
AMP PEAK 50(XQ28) WILD-TYPE	92	137	79	45

Figure S515. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.01

Table S516. Gene #50: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
AMP PEAK 50(XQ28) MUTATED	47	15	14	17
AMP PEAK 50(XQ28) WILD-TYPE	141	108	79	116

Figure S516. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0032

Table S517. Gene #50: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 50(XQ28) MUTATED	37	6	10	6	17	9	8
AMP PEAK 50(XQ28) WILD-TYPE	86	47	37	59	91	57	67

Figure S517. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.013

Table S518. Gene #50: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
AMP PEAK 50(XQ28) MUTATED	42	13	15	15	5
AMP PEAK 50(XQ28) WILD-TYPE	122	67	91	118	42

Figure S518. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.012

Table S519. Gene #50: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
AMP PEAK 50(XQ28) MUTATED	33	41	16
AMP PEAK 50(XQ28) WILD-TYPE	185	131	124

Figure S519. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.00065

Table S520. Gene #50: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
AMP PEAK 50(XQ28) MUTATED	35	13	14	8
AMP PEAK 50(XQ28) WILD-TYPE	81	85	78	84

Figure S520. Get High-res Image Gene #50: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MRNA_CNMF'

P value = 0.0328 (Fisher's exact test), Q value = 0.037

Table S521. Gene #51: 'del_1p36.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 1(1P36.21) MUTATED	2	6	0	0
DEL PEAK 1(1P36.21) WILD-TYPE	13	11	14	7

Figure S521. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0017 (Fisher's exact test), Q value = 0.0022

Table S522. Gene #51: 'del_1p36.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 1(1P36.21) MUTATED	3	5	0	0	0
DEL PEAK 1(1P36.21) WILD-TYPE	11	4	7	7	16

Figure S522. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S523. Gene #51: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 1(1P36.21) MUTATED	67	1	1	2
DEL PEAK 1(1P36.21) WILD-TYPE	141	177	98	52

Figure S523. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S524. Gene #51: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 1(1P36.21) MUTATED	33	19	8
DEL PEAK 1(1P36.21) WILD-TYPE	121	59	185

Figure S524. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S525. Gene #51: 'del_1p36.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 1(1P36.21) MUTATED	1	0	3	11	19	9	10
DEL PEAK 1(1P36.21) WILD-TYPE	38	81	49	45	65	59	43

Figure S525. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S526. Gene #51: 'del_1p36.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 1(1P36.21) MUTATED	1	35	9	8
DEL PEAK 1(1P36.21) WILD-TYPE	107	147	84	42

Figure S526. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S527. Gene #51: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 1(1P36.21) MUTATED	53	6	9	3
DEL PEAK 1(1P36.21) WILD-TYPE	135	117	84	130

Figure S527. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S528. Gene #51: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 1(1P36.21) MUTATED	42	1	9	4	12	3	0
DEL PEAK 1(1P36.21) WILD-TYPE	81	52	38	61	96	63	75

Figure S528. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S529. Gene #51: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 1(1P36.21) MUTATED	45	5	6	5	7
DEL PEAK 1(1P36.21) WILD-TYPE	119	75	100	128	40

Figure S529. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S530. Gene #51: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 1(1P36.21) MUTATED	16	49	3
DEL PEAK 1(1P36.21) WILD-TYPE	202	123	137

Figure S530. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00351 (Fisher's exact test), Q value = 0.0045

Table S531. Gene #51: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 1(1P36.21) MUTATED	21	6	22	11
DEL PEAK 1(1P36.21) WILD-TYPE	95	92	70	81

Figure S531. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.00084

Table S532. Gene #51: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 1(1P36.21) MUTATED	29	8	23
DEL PEAK 1(1P36.21) WILD-TYPE	134	124	80

Figure S532. Get High-res Image Gene #51: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.048

Table S533. Gene #52: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 2(1P36.11) MUTATED	1	5	0	0
DEL PEAK 2(1P36.11) WILD-TYPE	14	12	14	7

Figure S533. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.00775 (Fisher's exact test), Q value = 0.0095

Table S534. Gene #52: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 2(1P36.11) MUTATED	2	4	0	0	0
DEL PEAK 2(1P36.11) WILD-TYPE	12	5	7	7	16

Figure S534. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S535. Gene #52: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 2(1P36.11) MUTATED	79	1	1	2
DEL PEAK 2(1P36.11) WILD-TYPE	129	177	98	52

Figure S535. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S536. Gene #52: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 2(1P36.11) MUTATED	47	19	8
DEL PEAK 2(1P36.11) WILD-TYPE	107	59	185

Figure S536. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S537. Gene #52: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 2(1P36.11) MUTATED	2	0	5	16	22	9	11
DEL PEAK 2(1P36.11) WILD-TYPE	37	81	47	40	62	59	42

Figure S537. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S538. Gene #52: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 2(1P36.11) MUTATED	2	43	13	7
DEL PEAK 2(1P36.11) WILD-TYPE	106	139	80	43

Figure S538. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S539. Gene #52: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 2(1P36.11) MUTATED	65	6	9	3
DEL PEAK 2(1P36.11) WILD-TYPE	123	117	84	130

Figure S539. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S540. Gene #52: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 2(1P36.11) MUTATED	51	1	10	4	14	3	0
DEL PEAK 2(1P36.11) WILD-TYPE	72	52	37	61	94	63	75

Figure S540. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S541. Gene #52: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 2(1P36.11) MUTATED	58	4	6	6	6
DEL PEAK 2(1P36.11) WILD-TYPE	106	76	100	127	41

Figure S541. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S542. Gene #52: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 2(1P36.11) MUTATED	19	58	3
DEL PEAK 2(1P36.11) WILD-TYPE	199	114	137

Figure S542. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00072

Table S543. Gene #52: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 2(1P36.11) MUTATED	33	7	19	14
DEL PEAK 2(1P36.11) WILD-TYPE	83	91	73	78

Figure S543. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S544. Gene #52: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 2(1P36.11) MUTATED	43	8	22
DEL PEAK 2(1P36.11) WILD-TYPE	120	124	81

Figure S544. Get High-res Image Gene #52: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S545. Gene #53: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 3(2P25.3) MUTATED	25	0	1	0
DEL PEAK 3(2P25.3) WILD-TYPE	183	178	98	54

Figure S545. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.00079

Table S546. Gene #53: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 3(2P25.3) MUTATED	17	5	3
DEL PEAK 3(2P25.3) WILD-TYPE	137	73	190

Figure S546. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p25.3' versus 'RPPA_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.025

Table S547. Gene #53: 'del_2p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 3(2P25.3) MUTATED	1	1	0	6	6	1	4
DEL PEAK 3(2P25.3) WILD-TYPE	38	80	52	50	78	67	49

Figure S547. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S548. Gene #53: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 3(2P25.3) MUTATED	21	1	1	3
DEL PEAK 3(2P25.3) WILD-TYPE	167	122	92	130

Figure S548. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S549. Gene #53: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 3(2P25.3) MUTATED	16	1	3	0	3	3	0
DEL PEAK 3(2P25.3) WILD-TYPE	107	52	44	65	105	63	75

Figure S549. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S550. Gene #53: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 3(2P25.3) MUTATED	18	2	0	3	3
DEL PEAK 3(2P25.3) WILD-TYPE	146	78	106	130	44

Figure S550. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0028

Table S551. Gene #53: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 3(2P25.3) MUTATED	6	17	3
DEL PEAK 3(2P25.3) WILD-TYPE	212	155	137

Figure S551. Get High-res Image Gene #53: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.0097

Table S552. Gene #54: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 4(2Q22.1) MUTATED	0	5	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	15	12	14	7

Figure S552. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00518 (Fisher's exact test), Q value = 0.0064

Table S553. Gene #54: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 4(2Q22.1) MUTATED	1	4	0	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	13	5	7	7	16

Figure S553. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S554. Gene #54: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 4(2Q22.1) MUTATED	49	0	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	159	178	99	54

Figure S554. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S555. Gene #54: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 4(2Q22.1) MUTATED	24	13	6
DEL PEAK 4(2Q22.1) WILD-TYPE	130	65	187

Figure S555. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S556. Gene #54: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 4(2Q22.1) MUTATED	0	1	2	6	19	7	5
DEL PEAK 4(2Q22.1) WILD-TYPE	39	80	50	50	65	61	48

Figure S556. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.00088

Table S557. Gene #54: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 4(2Q22.1) MUTATED	1	22	13	4
DEL PEAK 4(2Q22.1) WILD-TYPE	107	160	80	46

Figure S557. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S558. Gene #54: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 4(2Q22.1) MUTATED	41	0	3	5
DEL PEAK 4(2Q22.1) WILD-TYPE	147	123	90	128

Figure S558. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S559. Gene #54: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 4(2Q22.1) MUTATED	32	0	3	0	9	5	0
DEL PEAK 4(2Q22.1) WILD-TYPE	91	53	44	65	99	61	75

Figure S559. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S560. Gene #54: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 4(2Q22.1) MUTATED	36	4	3	4	0
DEL PEAK 4(2Q22.1) WILD-TYPE	128	76	103	129	47

Figure S560. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S561. Gene #54: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 4(2Q22.1) MUTATED	14	29	4
DEL PEAK 4(2Q22.1) WILD-TYPE	204	143	136

Figure S561. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00037

Table S562. Gene #54: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 4(2Q22.1) MUTATED	25	6	4	7
DEL PEAK 4(2Q22.1) WILD-TYPE	91	92	88	85

Figure S562. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00502 (Fisher's exact test), Q value = 0.0062

Table S563. Gene #54: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 4(2Q22.1) MUTATED	27	7	8
DEL PEAK 4(2Q22.1) WILD-TYPE	136	125	95

Figure S563. Get High-res Image Gene #54: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S564. Gene #55: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 5(2Q37.3) MUTATED	49	1	0	2
DEL PEAK 5(2Q37.3) WILD-TYPE	159	177	99	52

Figure S564. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S565. Gene #55: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 5(2Q37.3) MUTATED	30	10	8
DEL PEAK 5(2Q37.3) WILD-TYPE	124	68	185

Figure S565. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0048

Table S566. Gene #55: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 5(2Q37.3) MUTATED	1	1	3	7	13	4	8
DEL PEAK 5(2Q37.3) WILD-TYPE	38	80	49	49	71	64	45

Figure S566. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0053 (Fisher's exact test), Q value = 0.0066

Table S567. Gene #55: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 5(2Q37.3) MUTATED	2	24	7	4
DEL PEAK 5(2Q37.3) WILD-TYPE	106	158	86	46

Figure S567. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S568. Gene #55: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 5(2Q37.3) MUTATED	37	1	6	7
DEL PEAK 5(2Q37.3) WILD-TYPE	151	122	87	126

Figure S568. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S569. Gene #55: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 5(2Q37.3) MUTATED	23	0	9	3	10	6	0
DEL PEAK 5(2Q37.3) WILD-TYPE	100	53	38	62	98	60	75

Figure S569. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00031

Table S570. Gene #55: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 5(2Q37.3) MUTATED	31	4	5	7	4
DEL PEAK 5(2Q37.3) WILD-TYPE	133	76	101	126	43

Figure S570. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0012

Table S571. Gene #55: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 5(2Q37.3) MUTATED	14	29	8
DEL PEAK 5(2Q37.3) WILD-TYPE	204	143	132

Figure S571. Get High-res Image Gene #55: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNA_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.048

Table S572. Gene #56: 'del_3p14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 6(3P14.2) MUTATED	1	5	0	0
DEL PEAK 6(3P14.2) WILD-TYPE	14	12	14	7

Figure S572. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00798 (Fisher's exact test), Q value = 0.0097

Table S573. Gene #56: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 6(3P14.2) MUTATED	2	4	0	0	0
DEL PEAK 6(3P14.2) WILD-TYPE	12	5	7	7	16

Figure S573. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S574. Gene #56: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 6(3P14.2) MUTATED	75	0	1	3
DEL PEAK 6(3P14.2) WILD-TYPE	133	178	98	51

Figure S574. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S575. Gene #56: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 6(3P14.2) MUTATED	45	17	6
DEL PEAK 6(3P14.2) WILD-TYPE	109	61	187

Figure S575. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S576. Gene #56: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 6(3P14.2) MUTATED	2	1	4	12	28	10	6
DEL PEAK 6(3P14.2) WILD-TYPE	37	80	48	44	56	58	47

Figure S576. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S577. Gene #56: 'del_3p14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 6(3P14.2) MUTATED	2	47	12	2
DEL PEAK 6(3P14.2) WILD-TYPE	106	135	81	48

Figure S577. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S578. Gene #56: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 6(3P14.2) MUTATED	65	3	6	4
DEL PEAK 6(3P14.2) WILD-TYPE	123	120	87	129

Figure S578. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S579. Gene #56: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 6(3P14.2) MUTATED	49	0	12	0	12	5	0
DEL PEAK 6(3P14.2) WILD-TYPE	74	53	35	65	96	61	75

Figure S579. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S580. Gene #56: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 6(3P14.2) MUTATED	56	5	6	4	6
DEL PEAK 6(3P14.2) WILD-TYPE	108	75	100	129	41

Figure S580. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S581. Gene #56: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 6(3P14.2) MUTATED	19	55	3
DEL PEAK 6(3P14.2) WILD-TYPE	199	117	137

Figure S581. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.0066

Table S582. Gene #56: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 6(3P14.2) MUTATED	28	7	13	18
DEL PEAK 6(3P14.2) WILD-TYPE	88	91	79	74

Figure S582. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S583. Gene #56: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 6(3P14.2) MUTATED	43	7	16
DEL PEAK 6(3P14.2) WILD-TYPE	120	125	87

Figure S583. Get High-res Image Gene #56: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S584. Gene #57: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 7(3Q13.31) MUTATED	36	2	2	3
DEL PEAK 7(3Q13.31) WILD-TYPE	172	176	97	51

Figure S584. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.013

Table S585. Gene #57: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 7(3Q13.31) MUTATED	19	9	8
DEL PEAK 7(3Q13.31) WILD-TYPE	135	69	185

Figure S585. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00367 (Fisher's exact test), Q value = 0.0047

Table S586. Gene #57: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 7(3Q13.31) MUTATED	1	21	8	4
DEL PEAK 7(3Q13.31) WILD-TYPE	107	161	85	46

Figure S586. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S587. Gene #57: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 7(3Q13.31) MUTATED	33	4	1	5
DEL PEAK 7(3Q13.31) WILD-TYPE	155	119	92	128

Figure S587. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S588. Gene #57: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 7(3Q13.31) MUTATED	28	2	4	0	3	5	1
DEL PEAK 7(3Q13.31) WILD-TYPE	95	51	43	65	105	61	74

Figure S588. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S589. Gene #57: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 7(3Q13.31) MUTATED	28	3	2	5	3
DEL PEAK 7(3Q13.31) WILD-TYPE	136	77	104	128	44

Figure S589. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S590. Gene #57: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 7(3Q13.31) MUTATED	10	27	4
DEL PEAK 7(3Q13.31) WILD-TYPE	208	145	136

Figure S590. Get High-res Image Gene #57: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.013

Table S591. Gene #58: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 8(4P16.3) MUTATED	1	6	0	0
DEL PEAK 8(4P16.3) WILD-TYPE	14	11	14	7

Figure S591. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0014

Table S592. Gene #58: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 8(4P16.3) MUTATED	2	5	0	0	0
DEL PEAK 8(4P16.3) WILD-TYPE	12	4	7	7	16

Figure S592. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S593. Gene #58: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 8(4P16.3) MUTATED	90	1	1	2
DEL PEAK 8(4P16.3) WILD-TYPE	118	177	98	52

Figure S593. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S594. Gene #58: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 8(4P16.3) MUTATED	55	18	9
DEL PEAK 8(4P16.3) WILD-TYPE	99	60	184

Figure S594. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S595. Gene #58: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 8(4P16.3) MUTATED	4	0	5	14	29	10	13
DEL PEAK 8(4P16.3) WILD-TYPE	35	81	47	42	55	58	40

Figure S595. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S596. Gene #58: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 8(4P16.3) MUTATED	5	46	15	9
DEL PEAK 8(4P16.3) WILD-TYPE	103	136	78	41

Figure S596. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S597. Gene #58: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 8(4P16.3) MUTATED	71	5	11	7
DEL PEAK 8(4P16.3) WILD-TYPE	117	118	82	126

Figure S597. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S598. Gene #58: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 8(4P16.3) MUTATED	55	1	15	2	14	6	1
DEL PEAK 8(4P16.3) WILD-TYPE	68	52	32	63	94	60	74

Figure S598. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S599. Gene #58: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 8(4P16.3) MUTATED	66	6	3	8	8
DEL PEAK 8(4P16.3) WILD-TYPE	98	74	103	125	39

Figure S599. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S600. Gene #58: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 8(4P16.3) MUTATED	23	62	6
DEL PEAK 8(4P16.3) WILD-TYPE	195	110	134

Figure S600. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S601. Gene #58: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 8(4P16.3) MUTATED	37	7	20	16
DEL PEAK 8(4P16.3) WILD-TYPE	79	91	72	76

Figure S601. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S602. Gene #58: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 8(4P16.3) MUTATED	44	11	25
DEL PEAK 8(4P16.3) WILD-TYPE	119	121	78

Figure S602. Get High-res Image Gene #58: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.31' versus 'MRNA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.013

Table S603. Gene #59: 'del_4p15.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 9(4P15.31) MUTATED	1	6	0	0
DEL PEAK 9(4P15.31) WILD-TYPE	14	11	14	7

Figure S603. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.0096 (Fisher's exact test), Q value = 0.012

Table S604. Gene #59: 'del_4p15.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 9(4P15.31) MUTATED	3	4	0	0	0
DEL PEAK 9(4P15.31) WILD-TYPE	11	5	7	7	16

Figure S604. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p15.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S605. Gene #59: 'del_4p15.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 9(4P15.31) MUTATED	95	1	0	3
DEL PEAK 9(4P15.31) WILD-TYPE	113	177	99	51

Figure S605. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S606. Gene #59: 'del_4p15.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 9(4P15.31) MUTATED	60	20	8
DEL PEAK 9(4P15.31) WILD-TYPE	94	58	185

Figure S606. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S607. Gene #59: 'del_4p15.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 9(4P15.31) MUTATED	4	1	4	19	30	10	12
DEL PEAK 9(4P15.31) WILD-TYPE	35	80	48	37	54	58	41

Figure S607. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p15.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S608. Gene #59: 'del_4p15.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 9(4P15.31) MUTATED	5	53	15	7
DEL PEAK 9(4P15.31) WILD-TYPE	103	129	78	43

Figure S608. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p15.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S609. Gene #59: 'del_4p15.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 9(4P15.31) MUTATED	76	5	11	7
DEL PEAK 9(4P15.31) WILD-TYPE	112	118	82	126

Figure S609. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S610. Gene #59: 'del_4p15.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 9(4P15.31) MUTATED	58	1	16	2	16	5	1
DEL PEAK 9(4P15.31) WILD-TYPE	65	52	31	63	92	61	74

Figure S610. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S611. Gene #59: 'del_4p15.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 9(4P15.31) MUTATED	73	5	4	7	8
DEL PEAK 9(4P15.31) WILD-TYPE	91	75	102	126	39

Figure S611. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S612. Gene #59: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 9(4P15.31) MUTATED	22	70	5
DEL PEAK 9(4P15.31) WILD-TYPE	196	102	135

Figure S612. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S613. Gene #59: 'del_4p15.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 9(4P15.31) MUTATED	43	6	20	18
DEL PEAK 9(4P15.31) WILD-TYPE	73	92	72	74

Figure S613. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S614. Gene #59: 'del_4p15.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 9(4P15.31) MUTATED	49	10	28
DEL PEAK 9(4P15.31) WILD-TYPE	114	122	75

Figure S614. Get High-res Image Gene #59: 'del_4p15.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.0047

Table S615. Gene #60: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 10(4Q22.1) MUTATED	1	7	0	0
DEL PEAK 10(4Q22.1) WILD-TYPE	14	10	14	7

Figure S615. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S616. Gene #60: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 10(4Q22.1) MUTATED	2	6	0	0	0
DEL PEAK 10(4Q22.1) WILD-TYPE	12	3	7	7	16

Figure S616. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S617. Gene #60: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 10(4Q22.1) MUTATED	105	0	0	1
DEL PEAK 10(4Q22.1) WILD-TYPE	103	178	99	53

Figure S617. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S618. Gene #60: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 10(4Q22.1) MUTATED	63	23	6
DEL PEAK 10(4Q22.1) WILD-TYPE	91	55	187

Figure S618. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S619. Gene #60: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 10(4Q22.1) MUTATED	3	2	3	16	32	14	14
DEL PEAK 10(4Q22.1) WILD-TYPE	36	79	49	40	52	54	39

Figure S619. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S620. Gene #60: 'del_4q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 10(4Q22.1) MUTATED	4	53	18	9
DEL PEAK 10(4Q22.1) WILD-TYPE	104	129	75	41

Figure S620. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S621. Gene #60: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 10(4Q22.1) MUTATED	87	4	9	6
DEL PEAK 10(4Q22.1) WILD-TYPE	101	119	84	127

Figure S621. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S622. Gene #60: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 10(4Q22.1) MUTATED	68	1	12	2	18	5	0
DEL PEAK 10(4Q22.1) WILD-TYPE	55	52	35	63	90	61	75

Figure S622. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S623. Gene #60: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 10(4Q22.1) MUTATED	74	4	8	6	11
DEL PEAK 10(4Q22.1) WILD-TYPE	90	76	98	127	36

Figure S623. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S624. Gene #60: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 10(4Q22.1) MUTATED	24	76	3
DEL PEAK 10(4Q22.1) WILD-TYPE	194	96	137

Figure S624. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S625. Gene #60: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 10(4Q22.1) MUTATED	44	5	22	19
DEL PEAK 10(4Q22.1) WILD-TYPE	72	93	70	73

Figure S625. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S626. Gene #60: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 10(4Q22.1) MUTATED	51	8	31
DEL PEAK 10(4Q22.1) WILD-TYPE	112	124	72

Figure S626. Get High-res Image Gene #60: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.0051

Table S627. Gene #61: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 11(4Q34.3) MUTATED	1	7	0	0
DEL PEAK 11(4Q34.3) WILD-TYPE	14	10	14	7

Figure S627. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00026

Table S628. Gene #61: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 11(4Q34.3) MUTATED	2	6	0	0	0
DEL PEAK 11(4Q34.3) WILD-TYPE	12	3	7	7	16

Figure S628. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S629. Gene #61: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 11(4Q34.3) MUTATED	125	2	0	3
DEL PEAK 11(4Q34.3) WILD-TYPE	83	176	99	51

Figure S629. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S630. Gene #61: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 11(4Q34.3) MUTATED	70	31	13
DEL PEAK 11(4Q34.3) WILD-TYPE	84	47	180

Figure S630. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S631. Gene #61: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 11(4Q34.3) MUTATED	5	3	7	19	36	17	17
DEL PEAK 11(4Q34.3) WILD-TYPE	34	78	45	37	48	51	36

Figure S631. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S632. Gene #61: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 11(4Q34.3) MUTATED	7	66	22	9
DEL PEAK 11(4Q34.3) WILD-TYPE	101	116	71	41

Figure S632. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S633. Gene #61: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 11(4Q34.3) MUTATED	102	8	13	7
DEL PEAK 11(4Q34.3) WILD-TYPE	86	115	80	126

Figure S633. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S634. Gene #61: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 11(4Q34.3) MUTATED	81	1	16	3	23	6	0
DEL PEAK 11(4Q34.3) WILD-TYPE	42	52	31	62	85	60	75

Figure S634. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S635. Gene #61: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 11(4Q34.3) MUTATED	90	10	10	7	10
DEL PEAK 11(4Q34.3) WILD-TYPE	74	70	96	126	37

Figure S635. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S636. Gene #61: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 11(4Q34.3) MUTATED	33	89	5
DEL PEAK 11(4Q34.3) WILD-TYPE	185	83	135

Figure S636. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S637. Gene #61: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 11(4Q34.3) MUTATED	55	8	29	20
DEL PEAK 11(4Q34.3) WILD-TYPE	61	90	63	72

Figure S637. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S638. Gene #61: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 11(4Q34.3) MUTATED	61	10	41
DEL PEAK 11(4Q34.3) WILD-TYPE	102	122	62

Figure S638. Get High-res Image Gene #61: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.014

Table S639. Gene #62: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 12(5Q12.1) MUTATED	1	6	0	0
DEL PEAK 12(5Q12.1) WILD-TYPE	14	11	14	7

Figure S639. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00984 (Fisher's exact test), Q value = 0.012

Table S640. Gene #62: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 12(5Q12.1) MUTATED	3	4	0	0	0
DEL PEAK 12(5Q12.1) WILD-TYPE	11	5	7	7	16

Figure S640. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S641. Gene #62: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 12(5Q12.1) MUTATED	107	0	0	4
DEL PEAK 12(5Q12.1) WILD-TYPE	101	178	99	50

Figure S641. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S642. Gene #62: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 12(5Q12.1) MUTATED	65	21	11
DEL PEAK 12(5Q12.1) WILD-TYPE	89	57	182

Figure S642. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S643. Gene #62: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 12(5Q12.1) MUTATED	0	2	5	23	32	11	13
DEL PEAK 12(5Q12.1) WILD-TYPE	39	79	47	33	52	57	40

Figure S643. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S644. Gene #62: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 12(5Q12.1) MUTATED	0	58	19	9
DEL PEAK 12(5Q12.1) WILD-TYPE	108	124	74	41

Figure S644. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S645. Gene #62: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 12(5Q12.1) MUTATED	87	6	9	8
DEL PEAK 12(5Q12.1) WILD-TYPE	101	117	84	125

Figure S645. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S646. Gene #62: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 12(5Q12.1) MUTATED	69	0	11	2	18	10	0
DEL PEAK 12(5Q12.1) WILD-TYPE	54	53	36	63	90	56	75

Figure S646. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S647. Gene #62: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 12(5Q12.1) MUTATED	77	5	7	9	12
DEL PEAK 12(5Q12.1) WILD-TYPE	87	75	99	124	35

Figure S647. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S648. Gene #62: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 12(5Q12.1) MUTATED	26	76	8
DEL PEAK 12(5Q12.1) WILD-TYPE	192	96	132

Figure S648. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S649. Gene #62: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 12(5Q12.1) MUTATED	52	9	18	16
DEL PEAK 12(5Q12.1) WILD-TYPE	64	89	74	76

Figure S649. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S650. Gene #62: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 12(5Q12.1) MUTATED	56	14	25
DEL PEAK 12(5Q12.1) WILD-TYPE	107	118	78

Figure S650. Get High-res Image Gene #62: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.035

Table S651. Gene #63: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 13(6Q26) MUTATED	1	3	0	0	0
DEL PEAK 13(6Q26) WILD-TYPE	13	6	7	7	16

Figure S651. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S652. Gene #63: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 13(6Q26) MUTATED	41	3	0	2
DEL PEAK 13(6Q26) WILD-TYPE	167	175	99	52

Figure S652. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S653. Gene #63: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 13(6Q26) MUTATED	26	13	1
DEL PEAK 13(6Q26) WILD-TYPE	128	65	192

Figure S653. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00052

Table S654. Gene #63: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 13(6Q26) MUTATED	2	0	1	7	14	5	7
DEL PEAK 13(6Q26) WILD-TYPE	37	81	51	49	70	63	46

Figure S654. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.002

Table S655. Gene #63: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 13(6Q26) MUTATED	1	23	7	5
DEL PEAK 13(6Q26) WILD-TYPE	107	159	86	45

Figure S655. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S656. Gene #63: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 13(6Q26) MUTATED	39	2	3	2
DEL PEAK 13(6Q26) WILD-TYPE	149	121	90	131

Figure S656. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S657. Gene #63: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 13(6Q26) MUTATED	36	1	3	0	5	0	1
DEL PEAK 13(6Q26) WILD-TYPE	87	52	44	65	103	66	74

Figure S657. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S658. Gene #63: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 13(6Q26) MUTATED	34	4	1	2	4
DEL PEAK 13(6Q26) WILD-TYPE	130	76	105	131	43

Figure S658. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S659. Gene #63: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 13(6Q26) MUTATED	10	34	1
DEL PEAK 13(6Q26) WILD-TYPE	208	138	139

Figure S659. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00029

Table S660. Gene #63: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 13(6Q26) MUTATED	21	2	11	5
DEL PEAK 13(6Q26) WILD-TYPE	95	96	81	87

Figure S660. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S661. Gene #63: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 13(6Q26) MUTATED	19	3	17
DEL PEAK 13(6Q26) WILD-TYPE	144	129	86

Figure S661. Get High-res Image Gene #63: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.00071

Table S662. Gene #64: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 14(7P22.3) MUTATED	0	7	0	0
DEL PEAK 14(7P22.3) WILD-TYPE	15	10	14	7

Figure S662. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.012

Table S663. Gene #64: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 14(7P22.3) MUTATED	3	4	0	0	0
DEL PEAK 14(7P22.3) WILD-TYPE	11	5	7	7	16

Figure S663. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S664. Gene #64: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 14(7P22.3) MUTATED	66	3	1	2
DEL PEAK 14(7P22.3) WILD-TYPE	142	175	98	52

Figure S664. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S665. Gene #64: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 14(7P22.3) MUTATED	39	19	5
DEL PEAK 14(7P22.3) WILD-TYPE	115	59	188

Figure S665. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S666. Gene #64: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 14(7P22.3) MUTATED	1	2	1	14	22	5	12
DEL PEAK 14(7P22.3) WILD-TYPE	38	79	51	42	62	63	41

Figure S666. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S667. Gene #64: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 14(7P22.3) MUTATED	2	36	9	10
DEL PEAK 14(7P22.3) WILD-TYPE	106	146	84	40

Figure S667. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S668. Gene #64: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 14(7P22.3) MUTATED	61	3	5	3
DEL PEAK 14(7P22.3) WILD-TYPE	127	120	88	130

Figure S668. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S669. Gene #64: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 14(7P22.3) MUTATED	51	0	9	0	8	4	0
DEL PEAK 14(7P22.3) WILD-TYPE	72	53	38	65	100	62	75

Figure S669. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S670. Gene #64: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 14(7P22.3) MUTATED	52	3	4	5	7
DEL PEAK 14(7P22.3) WILD-TYPE	112	77	102	128	40

Figure S670. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S671. Gene #64: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 14(7P22.3) MUTATED	14	55	2
DEL PEAK 14(7P22.3) WILD-TYPE	204	117	138

Figure S671. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0013

Table S672. Gene #64: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 14(7P22.3) MUTATED	26	4	15	14
DEL PEAK 14(7P22.3) WILD-TYPE	90	94	77	78

Figure S672. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S673. Gene #64: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 14(7P22.3) MUTATED	34	5	20
DEL PEAK 14(7P22.3) WILD-TYPE	129	127	83

Figure S673. Get High-res Image Gene #64: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S674. Gene #65: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 15(7Q11.22) MUTATED	41	0	0	0
DEL PEAK 15(7Q11.22) WILD-TYPE	167	178	99	54

Figure S674. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S675. Gene #65: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 15(7Q11.22) MUTATED	23	11	4
DEL PEAK 15(7Q11.22) WILD-TYPE	131	67	189

Figure S675. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q11.22' versus 'RPPA_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.00087

Table S676. Gene #65: 'del_7q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 15(7Q11.22) MUTATED	0	2	0	7	14	6	4
DEL PEAK 15(7Q11.22) WILD-TYPE	39	79	52	49	70	62	49

Figure S676. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.0032

Table S677. Gene #65: 'del_7q11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 15(7Q11.22) MUTATED	1	22	7	3
DEL PEAK 15(7Q11.22) WILD-TYPE	107	160	86	47

Figure S677. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S678. Gene #65: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 15(7Q11.22) MUTATED	35	1	3	2
DEL PEAK 15(7Q11.22) WILD-TYPE	153	122	90	131

Figure S678. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S679. Gene #65: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 15(7Q11.22) MUTATED	27	0	4	0	7	3	0
DEL PEAK 15(7Q11.22) WILD-TYPE	96	53	43	65	101	63	75

Figure S679. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S680. Gene #65: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 15(7Q11.22) MUTATED	33	1	1	3	2
DEL PEAK 15(7Q11.22) WILD-TYPE	131	79	105	130	45

Figure S680. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S681. Gene #65: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 15(7Q11.22) MUTATED	9	29	2
DEL PEAK 15(7Q11.22) WILD-TYPE	209	143	138

Figure S681. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.013

Table S682. Gene #65: 'del_7q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 15(7Q11.22) MUTATED	18	3	6	9
DEL PEAK 15(7Q11.22) WILD-TYPE	98	95	86	83

Figure S682. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.0058

Table S683. Gene #65: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 15(7Q11.22) MUTATED	22	4	10
DEL PEAK 15(7Q11.22) WILD-TYPE	141	128	93

Figure S683. Get High-res Image Gene #65: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S684. Gene #66: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 16(7Q31.1) MUTATED	55	0	0	0
DEL PEAK 16(7Q31.1) WILD-TYPE	153	178	99	54

Figure S684. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S685. Gene #66: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 16(7Q31.1) MUTATED	32	16	2
DEL PEAK 16(7Q31.1) WILD-TYPE	122	62	191

Figure S685. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S686. Gene #66: 'del_7q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 16(7Q31.1) MUTATED	1	1	1	8	23	6	8
DEL PEAK 16(7Q31.1) WILD-TYPE	38	80	51	48	61	62	45

Figure S686. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S687. Gene #66: 'del_7q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 16(7Q31.1) MUTATED	1	31	10	6
DEL PEAK 16(7Q31.1) WILD-TYPE	107	151	83	44

Figure S687. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S688. Gene #66: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 16(7Q31.1) MUTATED	52	0	2	1
DEL PEAK 16(7Q31.1) WILD-TYPE	136	123	91	132

Figure S688. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S689. Gene #66: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 16(7Q31.1) MUTATED	44	0	4	0	5	2	0
DEL PEAK 16(7Q31.1) WILD-TYPE	79	53	43	65	103	64	75

Figure S689. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S690. Gene #66: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 16(7Q31.1) MUTATED	45	1	2	3	3
DEL PEAK 16(7Q31.1) WILD-TYPE	119	79	104	130	44

Figure S690. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S691. Gene #66: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 16(7Q31.1) MUTATED	8	44	2
DEL PEAK 16(7Q31.1) WILD-TYPE	210	128	138

Figure S691. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00022

Table S692. Gene #66: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 16(7Q31.1) MUTATED	26	3	8	10
DEL PEAK 16(7Q31.1) WILD-TYPE	90	95	84	82

Figure S692. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00022

Table S693. Gene #66: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 16(7Q31.1) MUTATED	27	4	16
DEL PEAK 16(7Q31.1) WILD-TYPE	136	128	87

Figure S693. Get High-res Image Gene #66: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S694. Gene #67: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 17(7Q36.1) MUTATED	62	0	1	0
DEL PEAK 17(7Q36.1) WILD-TYPE	146	178	98	54

Figure S694. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S695. Gene #67: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 17(7Q36.1) MUTATED	34	18	2
DEL PEAK 17(7Q36.1) WILD-TYPE	120	60	191

Figure S695. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S696. Gene #67: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 17(7Q36.1) MUTATED	1	1	1	10	23	8	8
DEL PEAK 17(7Q36.1) WILD-TYPE	38	80	51	46	61	60	45

Figure S696. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S697. Gene #67: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 17(7Q36.1) MUTATED	1	35	11	5
DEL PEAK 17(7Q36.1) WILD-TYPE	107	147	82	45

Figure S697. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S698. Gene #67: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 17(7Q36.1) MUTATED	58	0	4	1
DEL PEAK 17(7Q36.1) WILD-TYPE	130	123	89	132

Figure S698. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S699. Gene #67: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 17(7Q36.1) MUTATED	50	0	7	0	4	2	0
DEL PEAK 17(7Q36.1) WILD-TYPE	73	53	40	65	104	64	75

Figure S699. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S700. Gene #67: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 17(7Q36.1) MUTATED	51	1	3	3	4
DEL PEAK 17(7Q36.1) WILD-TYPE	113	79	103	130	43

Figure S700. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S701. Gene #67: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 17(7Q36.1) MUTATED	9	51	2
DEL PEAK 17(7Q36.1) WILD-TYPE	209	121	138

Figure S701. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S702. Gene #67: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 17(7Q36.1) MUTATED	26	3	9	12
DEL PEAK 17(7Q36.1) WILD-TYPE	90	95	83	80

Figure S702. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S703. Gene #67: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 17(7Q36.1) MUTATED	31	3	16
DEL PEAK 17(7Q36.1) WILD-TYPE	132	129	87

Figure S703. Get High-res Image Gene #67: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.00218 (Fisher's exact test), Q value = 0.0028

Table S704. Gene #68: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 18(8P23.2) MUTATED	0	6	0	0
DEL PEAK 18(8P23.2) WILD-TYPE	15	11	14	7

Figure S704. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S705. Gene #68: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 18(8P23.2) MUTATED	0	6	0	0	0
DEL PEAK 18(8P23.2) WILD-TYPE	14	3	7	7	16

Figure S705. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S706. Gene #68: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 18(8P23.2) MUTATED	111	3	2	3
DEL PEAK 18(8P23.2) WILD-TYPE	97	175	97	51

Figure S706. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S707. Gene #68: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 18(8P23.2) MUTATED	71	29	5
DEL PEAK 18(8P23.2) WILD-TYPE	83	49	188

Figure S707. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S708. Gene #68: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 18(8P23.2) MUTATED	3	2	6	16	36	17	18
DEL PEAK 18(8P23.2) WILD-TYPE	36	79	46	40	48	51	35

Figure S708. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S709. Gene #68: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 18(8P23.2) MUTATED	3	62	21	12
DEL PEAK 18(8P23.2) WILD-TYPE	105	120	72	38

Figure S709. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S710. Gene #68: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 18(8P23.2) MUTATED	98	5	11	4
DEL PEAK 18(8P23.2) WILD-TYPE	90	118	82	129

Figure S710. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S711. Gene #68: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 18(8P23.2) MUTATED	77	0	20	1	14	5	1
DEL PEAK 18(8P23.2) WILD-TYPE	46	53	27	64	94	61	74

Figure S711. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S712. Gene #68: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 18(8P23.2) MUTATED	85	4	10	7	10
DEL PEAK 18(8P23.2) WILD-TYPE	79	76	96	126	37

Figure S712. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S713. Gene #68: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 18(8P23.2) MUTATED	20	91	5
DEL PEAK 18(8P23.2) WILD-TYPE	198	81	135

Figure S713. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S714. Gene #68: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 18(8P23.2) MUTATED	49	5	20	25
DEL PEAK 18(8P23.2) WILD-TYPE	67	93	72	67

Figure S714. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S715. Gene #68: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 18(8P23.2) MUTATED	58	6	35
DEL PEAK 18(8P23.2) WILD-TYPE	105	126	68

Figure S715. Get High-res Image Gene #68: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.2' versus 'MRNA_CNMF'

P value = 0.00258 (Fisher's exact test), Q value = 0.0033

Table S716. Gene #69: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 19(8P21.2) MUTATED	0	6	0	0
DEL PEAK 19(8P21.2) WILD-TYPE	15	11	14	7

Figure S716. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S717. Gene #69: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 19(8P21.2) MUTATED	0	6	0	0	0
DEL PEAK 19(8P21.2) WILD-TYPE	14	3	7	7	16

Figure S717. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S718. Gene #69: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 19(8P21.2) MUTATED	112	2	0	3
DEL PEAK 19(8P21.2) WILD-TYPE	96	176	99	51

Figure S718. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S719. Gene #69: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 19(8P21.2) MUTATED	73	28	2
DEL PEAK 19(8P21.2) WILD-TYPE	81	50	191

Figure S719. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S720. Gene #69: 'del_8p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 19(8P21.2) MUTATED	2	1	6	18	33	17	17
DEL PEAK 19(8P21.2) WILD-TYPE	37	80	46	38	51	51	36

Figure S720. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S721. Gene #69: 'del_8p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 19(8P21.2) MUTATED	1	62	20	11
DEL PEAK 19(8P21.2) WILD-TYPE	107	120	73	39

Figure S721. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S722. Gene #69: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 19(8P21.2) MUTATED	101	4	10	1
DEL PEAK 19(8P21.2) WILD-TYPE	87	119	83	132

Figure S722. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S723. Gene #69: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 19(8P21.2) MUTATED	80	0	20	1	12	3	0
DEL PEAK 19(8P21.2) WILD-TYPE	43	53	27	64	96	63	75

Figure S723. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S724. Gene #69: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 19(8P21.2) MUTATED	87	4	11	3	9
DEL PEAK 19(8P21.2) WILD-TYPE	77	76	95	130	38

Figure S724. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S725. Gene #69: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 19(8P21.2) MUTATED	17	95	2
DEL PEAK 19(8P21.2) WILD-TYPE	201	77	138

Figure S725. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S726. Gene #69: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 19(8P21.2) MUTATED	49	2	21	26
DEL PEAK 19(8P21.2) WILD-TYPE	67	96	71	66

Figure S726. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S727. Gene #69: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 19(8P21.2) MUTATED	59	4	35
DEL PEAK 19(8P21.2) WILD-TYPE	104	128	68

Figure S727. Get High-res Image Gene #69: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0498 (Fisher's exact test), Q value = 0.056

Table S728. Gene #70: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 20(9P23) MUTATED	2	3	0	0	0
DEL PEAK 20(9P23) WILD-TYPE	12	6	7	7	16

Figure S728. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S729. Gene #70: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 20(9P23) MUTATED	75	1	0	4
DEL PEAK 20(9P23) WILD-TYPE	133	177	99	50

Figure S729. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S730. Gene #70: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 20(9P23) MUTATED	43	19	9
DEL PEAK 20(9P23) WILD-TYPE	111	59	184

Figure S730. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00046

Table S731. Gene #70: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 20(9P23) MUTATED	3	2	4	10	20	11	12
DEL PEAK 20(9P23) WILD-TYPE	36	79	48	46	64	57	41

Figure S731. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00077

Table S732. Gene #70: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 20(9P23) MUTATED	4	36	15	7
DEL PEAK 20(9P23) WILD-TYPE	104	146	78	43

Figure S732. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S733. Gene #70: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 20(9P23) MUTATED	56	4	9	11
DEL PEAK 20(9P23) WILD-TYPE	132	119	84	122

Figure S733. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S734. Gene #70: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 20(9P23) MUTATED	42	0	14	2	12	9	1
DEL PEAK 20(9P23) WILD-TYPE	81	53	33	63	96	57	74

Figure S734. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S735. Gene #70: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 20(9P23) MUTATED	51	3	5	12	8
DEL PEAK 20(9P23) WILD-TYPE	113	77	101	121	39

Figure S735. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S736. Gene #70: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 20(9P23) MUTATED	13	55	11
DEL PEAK 20(9P23) WILD-TYPE	205	117	129

Figure S736. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.0051

Table S737. Gene #70: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 20(9P23) MUTATED	32	10	16	11
DEL PEAK 20(9P23) WILD-TYPE	84	88	76	81

Figure S737. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.013

Table S738. Gene #70: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 20(9P23) MUTATED	37	13	19
DEL PEAK 20(9P23) WILD-TYPE	126	119	84

Figure S738. Get High-res Image Gene #70: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.2' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S739. Gene #71: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 21(9Q21.2) MUTATED	0	9	0	0
DEL PEAK 21(9Q21.2) WILD-TYPE	15	8	14	7

Figure S739. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S740. Gene #71: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 21(9Q21.2) MUTATED	2	7	0	0	0
DEL PEAK 21(9Q21.2) WILD-TYPE	12	2	7	7	16

Figure S740. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S741. Gene #71: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 21(9Q21.2) MUTATED	123	1	1	4
DEL PEAK 21(9Q21.2) WILD-TYPE	85	177	98	50

Figure S741. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S742. Gene #71: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 21(9Q21.2) MUTATED	70	25	18
DEL PEAK 21(9Q21.2) WILD-TYPE	84	53	175

Figure S742. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S743. Gene #71: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 21(9Q21.2) MUTATED	5	3	7	20	31	16	17
DEL PEAK 21(9Q21.2) WILD-TYPE	34	78	45	36	53	52	36

Figure S743. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S744. Gene #71: 'del_9q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 21(9Q21.2) MUTATED	7	64	20	8
DEL PEAK 21(9Q21.2) WILD-TYPE	101	118	73	42

Figure S744. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S745. Gene #71: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 21(9Q21.2) MUTATED	96	9	9	15
DEL PEAK 21(9Q21.2) WILD-TYPE	92	114	84	118

Figure S745. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S746. Gene #71: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 21(9Q21.2) MUTATED	77	0	16	3	19	13	1
DEL PEAK 21(9Q21.2) WILD-TYPE	46	53	31	62	89	53	74

Figure S746. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S747. Gene #71: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 21(9Q21.2) MUTATED	90	5	5	15	11
DEL PEAK 21(9Q21.2) WILD-TYPE	74	75	101	118	36

Figure S747. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S748. Gene #71: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 21(9Q21.2) MUTATED	30	82	14
DEL PEAK 21(9Q21.2) WILD-TYPE	188	90	126

Figure S748. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S749. Gene #71: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 21(9Q21.2) MUTATED	52	15	24	19
DEL PEAK 21(9Q21.2) WILD-TYPE	64	83	68	73

Figure S749. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S750. Gene #71: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 21(9Q21.2) MUTATED	60	20	30
DEL PEAK 21(9Q21.2) WILD-TYPE	103	112	73

Figure S750. Get High-res Image Gene #71: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S751. Gene #72: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 22(9Q34.2) MUTATED	0	9	0	0
DEL PEAK 22(9Q34.2) WILD-TYPE	15	8	14	7

Figure S751. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S752. Gene #72: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 22(9Q34.2) MUTATED	2	7	0	0	0
DEL PEAK 22(9Q34.2) WILD-TYPE	12	2	7	7	16

Figure S752. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S753. Gene #72: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 22(9Q34.2) MUTATED	127	1	1	3
DEL PEAK 22(9Q34.2) WILD-TYPE	81	177	98	51

Figure S753. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S754. Gene #72: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 22(9Q34.2) MUTATED	68	30	16
DEL PEAK 22(9Q34.2) WILD-TYPE	86	48	177

Figure S754. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S755. Gene #72: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 22(9Q34.2) MUTATED	5	2	9	21	35	17	14
DEL PEAK 22(9Q34.2) WILD-TYPE	34	79	43	35	49	51	39

Figure S755. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S756. Gene #72: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 22(9Q34.2) MUTATED	7	64	25	7
DEL PEAK 22(9Q34.2) WILD-TYPE	101	118	68	43

Figure S756. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S757. Gene #72: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 22(9Q34.2) MUTATED	97	9	11	14
DEL PEAK 22(9Q34.2) WILD-TYPE	91	114	82	119

Figure S757. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S758. Gene #72: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 22(9Q34.2) MUTATED	75	0	16	3	22	14	1
DEL PEAK 22(9Q34.2) WILD-TYPE	48	53	31	62	86	52	74

Figure S758. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S759. Gene #72: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 22(9Q34.2) MUTATED	90	6	6	16	11
DEL PEAK 22(9Q34.2) WILD-TYPE	74	74	100	117	36

Figure S759. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S760. Gene #72: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 22(9Q34.2) MUTATED	34	81	14
DEL PEAK 22(9Q34.2) WILD-TYPE	184	91	126

Figure S760. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00025

Table S761. Gene #72: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 22(9Q34.2) MUTATED	50	16	22	23
DEL PEAK 22(9Q34.2) WILD-TYPE	66	82	70	69

Figure S761. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S762. Gene #72: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 22(9Q34.2) MUTATED	63	20	28
DEL PEAK 22(9Q34.2) WILD-TYPE	100	112	75

Figure S762. Get High-res Image Gene #72: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S763. Gene #73: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 23(10Q21.1) MUTATED	49	0	0	1
DEL PEAK 23(10Q21.1) WILD-TYPE	159	178	99	53

Figure S763. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S764. Gene #73: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 23(10Q21.1) MUTATED	33	13	2
DEL PEAK 23(10Q21.1) WILD-TYPE	121	65	191

Figure S764. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q21.1' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00011

Table S765. Gene #73: 'del_10q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 23(10Q21.1) MUTATED	0	1	2	9	17	8	5
DEL PEAK 23(10Q21.1) WILD-TYPE	39	80	50	47	67	60	48

Figure S765. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q21.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S766. Gene #73: 'del_10q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 23(10Q21.1) MUTATED	0	30	10	2
DEL PEAK 23(10Q21.1) WILD-TYPE	108	152	83	48

Figure S766. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S767. Gene #73: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 23(10Q21.1) MUTATED	42	1	4	3
DEL PEAK 23(10Q21.1) WILD-TYPE	146	122	89	130

Figure S767. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S768. Gene #73: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 23(10Q21.1) MUTATED	36	0	3	1	7	3	0
DEL PEAK 23(10Q21.1) WILD-TYPE	87	53	44	64	101	63	75

Figure S768. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S769. Gene #73: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 23(10Q21.1) MUTATED	41	2	1	2	4
DEL PEAK 23(10Q21.1) WILD-TYPE	123	78	105	131	43

Figure S769. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S770. Gene #73: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 23(10Q21.1) MUTATED	9	38	3
DEL PEAK 23(10Q21.1) WILD-TYPE	209	134	137

Figure S770. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S771. Gene #73: 'del_10q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 23(10Q21.1) MUTATED	29	3	7	8
DEL PEAK 23(10Q21.1) WILD-TYPE	87	95	85	84

Figure S771. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S772. Gene #73: 'del_10q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 23(10Q21.1) MUTATED	31	3	13
DEL PEAK 23(10Q21.1) WILD-TYPE	132	129	90

Figure S772. Get High-res Image Gene #73: 'del_10q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S773. Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 24(10Q23.31) MUTATED	72	0	2	4
DEL PEAK 24(10Q23.31) WILD-TYPE	136	178	97	50

Figure S773. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S774. Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 24(10Q23.31) MUTATED	40	22	7
DEL PEAK 24(10Q23.31) WILD-TYPE	114	56	186

Figure S774. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S775. Gene #74: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 24(10Q23.31) MUTATED	3	1	6	11	22	11	8
DEL PEAK 24(10Q23.31) WILD-TYPE	36	80	46	45	62	57	45

Figure S775. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S776. Gene #74: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 24(10Q23.31) MUTATED	3	40	14	5
DEL PEAK 24(10Q23.31) WILD-TYPE	105	142	79	45

Figure S776. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S777. Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 24(10Q23.31) MUTATED	59	2	9	7
DEL PEAK 24(10Q23.31) WILD-TYPE	129	121	84	126

Figure S777. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S778. Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 24(10Q23.31) MUTATED	48	0	7	3	12	5	2
DEL PEAK 24(10Q23.31) WILD-TYPE	75	53	40	62	96	61	73

Figure S778. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S779. Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 24(10Q23.31) MUTATED	54	4	5	6	8
DEL PEAK 24(10Q23.31) WILD-TYPE	110	76	101	127	39

Figure S779. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S780. Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 24(10Q23.31) MUTATED	18	52	7
DEL PEAK 24(10Q23.31) WILD-TYPE	200	120	133

Figure S780. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S781. Gene #74: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 24(10Q23.31) MUTATED	33	6	12	17
DEL PEAK 24(10Q23.31) WILD-TYPE	83	92	80	75

Figure S781. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S782. Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 24(10Q23.31) MUTATED	40	8	20
DEL PEAK 24(10Q23.31) WILD-TYPE	123	124	83

Figure S782. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S783. Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 25(11P15.5) MUTATED	99	1	0	4
DEL PEAK 25(11P15.5) WILD-TYPE	109	177	99	50

Figure S783. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S784. Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 25(11P15.5) MUTATED	59	28	8
DEL PEAK 25(11P15.5) WILD-TYPE	95	50	185

Figure S784. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S785. Gene #75: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 25(11P15.5) MUTATED	3	2	6	16	32	10	10
DEL PEAK 25(11P15.5) WILD-TYPE	36	79	46	40	52	58	43

Figure S785. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S786. Gene #75: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 25(11P15.5) MUTATED	5	54	13	7
DEL PEAK 25(11P15.5) WILD-TYPE	103	128	80	43

Figure S786. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S787. Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 25(11P15.5) MUTATED	78	5	10	10
DEL PEAK 25(11P15.5) WILD-TYPE	110	118	83	123

Figure S787. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S788. Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 25(11P15.5) MUTATED	58	1	18	0	15	9	2
DEL PEAK 25(11P15.5) WILD-TYPE	65	52	29	65	93	57	73

Figure S788. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S789. Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 25(11P15.5) MUTATED	74	4	4	13	8
DEL PEAK 25(11P15.5) WILD-TYPE	90	76	102	120	39

Figure S789. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S790. Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 25(11P15.5) MUTATED	20	72	11
DEL PEAK 25(11P15.5) WILD-TYPE	198	100	129

Figure S790. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S791. Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 25(11P15.5) MUTATED	50	10	15	20
DEL PEAK 25(11P15.5) WILD-TYPE	66	88	77	72

Figure S791. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S792. Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 25(11P15.5) MUTATED	60	14	21
DEL PEAK 25(11P15.5) WILD-TYPE	103	118	82

Figure S792. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S793. Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 26(11Q14.1) MUTATED	65	0	0	4
DEL PEAK 26(11Q14.1) WILD-TYPE	143	178	99	50

Figure S793. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S794. Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 26(11Q14.1) MUTATED	42	17	6
DEL PEAK 26(11Q14.1) WILD-TYPE	112	61	187

Figure S794. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q14.1' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.7e-05

Table S795. Gene #76: 'del_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 26(11Q14.1) MUTATED	3	2	4	12	23	8	4
DEL PEAK 26(11Q14.1) WILD-TYPE	36	79	48	44	61	60	49

Figure S795. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S796. Gene #76: 'del_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 26(11Q14.1) MUTATED	3	44	7	2
DEL PEAK 26(11Q14.1) WILD-TYPE	105	138	86	48

Figure S796. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S797. Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 26(11Q14.1) MUTATED	53	3	6	6
DEL PEAK 26(11Q14.1) WILD-TYPE	135	120	87	127

Figure S797. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S798. Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 26(11Q14.1) MUTATED	42	1	12	1	8	4	0
DEL PEAK 26(11Q14.1) WILD-TYPE	81	52	35	64	100	62	75

Figure S798. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S799. Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 26(11Q14.1) MUTATED	53	3	2	8	3
DEL PEAK 26(11Q14.1) WILD-TYPE	111	77	104	125	44

Figure S799. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S800. Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 26(11Q14.1) MUTATED	10	52	7
DEL PEAK 26(11Q14.1) WILD-TYPE	208	120	133

Figure S800. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S801. Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 26(11Q14.1) MUTATED	34	7	9	14
DEL PEAK 26(11Q14.1) WILD-TYPE	82	91	83	78

Figure S801. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S802. Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 26(11Q14.1) MUTATED	44	7	13
DEL PEAK 26(11Q14.1) WILD-TYPE	119	125	90

Figure S802. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S803. Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 27(11Q25) MUTATED	89	2	0	3
DEL PEAK 27(11Q25) WILD-TYPE	119	176	99	51

Figure S803. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S804. Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 27(11Q25) MUTATED	58	19	8
DEL PEAK 27(11Q25) WILD-TYPE	96	59	185

Figure S804. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S805. Gene #77: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 27(11Q25) MUTATED	4	3	9	15	31	9	7
DEL PEAK 27(11Q25) WILD-TYPE	35	78	43	41	53	59	46

Figure S805. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q25' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S806. Gene #77: 'del_11q25' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 27(11Q25) MUTATED	5	55	15	3
DEL PEAK 27(11Q25) WILD-TYPE	103	127	78	47

Figure S806. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S807. Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 27(11Q25) MUTATED	68	6	10	9
DEL PEAK 27(11Q25) WILD-TYPE	120	117	83	124

Figure S807. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S808. Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 27(11Q25) MUTATED	53	1	14	2	16	6	1
DEL PEAK 27(11Q25) WILD-TYPE	70	52	33	63	92	60	74

Figure S808. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S809. Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 27(11Q25) MUTATED	62	7	5	11	7
DEL PEAK 27(11Q25) WILD-TYPE	102	73	101	122	40

Figure S809. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S810. Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 27(11Q25) MUTATED	20	64	8
DEL PEAK 27(11Q25) WILD-TYPE	198	108	132

Figure S810. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 4e-04

Table S811. Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 27(11Q25) MUTATED	39	10	15	19
DEL PEAK 27(11Q25) WILD-TYPE	77	88	77	73

Figure S811. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S812. Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 27(11Q25) MUTATED	51	11	21
DEL PEAK 27(11Q25) WILD-TYPE	112	121	82

Figure S812. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S813. Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 28(12Q23.1) MUTATED	55	0	0	1
DEL PEAK 28(12Q23.1) WILD-TYPE	153	178	99	53

Figure S813. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S814. Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 28(12Q23.1) MUTATED	33	13	2
DEL PEAK 28(12Q23.1) WILD-TYPE	121	65	191

Figure S814. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S815. Gene #78: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 28(12Q23.1) MUTATED	1	0	3	8	16	9	11
DEL PEAK 28(12Q23.1) WILD-TYPE	38	81	49	48	68	59	42

Figure S815. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S816. Gene #78: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 28(12Q23.1) MUTATED	0	32	10	6
DEL PEAK 28(12Q23.1) WILD-TYPE	108	150	83	44

Figure S816. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S817. Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 28(12Q23.1) MUTATED	47	1	5	3
DEL PEAK 28(12Q23.1) WILD-TYPE	141	122	88	130

Figure S817. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S818. Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 28(12Q23.1) MUTATED	39	0	9	0	3	5	0
DEL PEAK 28(12Q23.1) WILD-TYPE	84	53	38	65	105	61	75

Figure S818. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S819. Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 28(12Q23.1) MUTATED	36	4	4	2	8
DEL PEAK 28(12Q23.1) WILD-TYPE	128	76	102	131	39

Figure S819. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S820. Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 28(12Q23.1) MUTATED	10	44	0
DEL PEAK 28(12Q23.1) WILD-TYPE	208	128	140

Figure S820. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S821. Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 28(12Q23.1) MUTATED	27	2	8	10
DEL PEAK 28(12Q23.1) WILD-TYPE	89	96	84	82

Figure S821. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S822. Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 28(12Q23.1) MUTATED	29	2	16
DEL PEAK 28(12Q23.1) WILD-TYPE	134	130	87

Figure S822. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S823. Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 29(12Q24.33) MUTATED	64	0	0	2
DEL PEAK 29(12Q24.33) WILD-TYPE	144	178	99	52

Figure S823. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S824. Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 29(12Q24.33) MUTATED	42	15	4
DEL PEAK 29(12Q24.33) WILD-TYPE	112	63	189

Figure S824. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S825. Gene #79: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 29(12Q24.33) MUTATED	1	1	4	9	19	9	10
DEL PEAK 29(12Q24.33) WILD-TYPE	38	80	48	47	65	59	43

Figure S825. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S826. Gene #79: 'del_12q24.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 29(12Q24.33) MUTATED	0	36	12	5
DEL PEAK 29(12Q24.33) WILD-TYPE	108	146	81	45

Figure S826. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S827. Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 29(12Q24.33) MUTATED	59	0	4	3
DEL PEAK 29(12Q24.33) WILD-TYPE	129	123	89	130

Figure S827. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S828. Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 29(12Q24.33) MUTATED	45	0	8	0	9	4	0
DEL PEAK 29(12Q24.33) WILD-TYPE	78	53	39	65	99	62	75

Figure S828. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S829. Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 29(12Q24.33) MUTATED	48	3	3	3	7
DEL PEAK 29(12Q24.33) WILD-TYPE	116	77	103	130	40

Figure S829. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S830. Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 29(12Q24.33) MUTATED	13	49	2
DEL PEAK 29(12Q24.33) WILD-TYPE	205	123	138

Figure S830. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S831. Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 29(12Q24.33) MUTATED	33	3	9	14
DEL PEAK 29(12Q24.33) WILD-TYPE	83	95	83	78

Figure S831. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S832. Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 29(12Q24.33) MUTATED	36	5	18
DEL PEAK 29(12Q24.33) WILD-TYPE	127	127	85

Figure S832. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.045

Table S833. Gene #80: 'del_13q11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 30(13Q11) MUTATED	3	3	0	0	0
DEL PEAK 30(13Q11) WILD-TYPE	11	6	7	7	16

Figure S833. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S834. Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 30(13Q11) MUTATED	94	1	2	1
DEL PEAK 30(13Q11) WILD-TYPE	114	177	97	53

Figure S834. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S835. Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 30(13Q11) MUTATED	53	18	13
DEL PEAK 30(13Q11) WILD-TYPE	101	60	180

Figure S835. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q11' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S836. Gene #80: 'del_13q11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 30(13Q11) MUTATED	3	2	5	17	24	9	14
DEL PEAK 30(13Q11) WILD-TYPE	36	79	47	39	60	59	39

Figure S836. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q11' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S837. Gene #80: 'del_13q11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 30(13Q11) MUTATED	4	45	17	8
DEL PEAK 30(13Q11) WILD-TYPE	104	137	76	42

Figure S837. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S838. Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 30(13Q11) MUTATED	70	10	5	13
DEL PEAK 30(13Q11) WILD-TYPE	118	113	88	120

Figure S838. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S839. Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 30(13Q11) MUTATED	52	1	11	0	21	12	1
DEL PEAK 30(13Q11) WILD-TYPE	71	52	36	65	87	54	74

Figure S839. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S840. Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 30(13Q11) MUTATED	61	8	6	13	9
DEL PEAK 30(13Q11) WILD-TYPE	103	72	100	120	38

Figure S840. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S841. Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 30(13Q11) MUTATED	28	58	11
DEL PEAK 30(13Q11) WILD-TYPE	190	114	129

Figure S841. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.0057

Table S842. Gene #80: 'del_13q11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 30(13Q11) MUTATED	37	14	19	13
DEL PEAK 30(13Q11) WILD-TYPE	79	84	73	79

Figure S842. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00661 (Fisher's exact test), Q value = 0.0081

Table S843. Gene #80: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 30(13Q11) MUTATED	39	16	28
DEL PEAK 30(13Q11) WILD-TYPE	124	116	75

Figure S843. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S844. Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 31(13Q14.2) MUTATED	100	3	1	2
DEL PEAK 31(13Q14.2) WILD-TYPE	108	175	98	52

Figure S844. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S845. Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 31(13Q14.2) MUTATED	54	22	17
DEL PEAK 31(13Q14.2) WILD-TYPE	100	56	176

Figure S845. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S846. Gene #81: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 31(13Q14.2) MUTATED	4	5	6	18	28	9	13
DEL PEAK 31(13Q14.2) WILD-TYPE	35	76	46	38	56	59	40

Figure S846. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S847. Gene #81: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 31(13Q14.2) MUTATED	6	50	18	9
DEL PEAK 31(13Q14.2) WILD-TYPE	102	132	75	41

Figure S847. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S848. Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 31(13Q14.2) MUTATED	71	12	7	16
DEL PEAK 31(13Q14.2) WILD-TYPE	117	111	86	117

Figure S848. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S849. Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 31(13Q14.2) MUTATED	47	3	15	0	25	14	2
DEL PEAK 31(13Q14.2) WILD-TYPE	76	50	32	65	83	52	73

Figure S849. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S850. Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 31(13Q14.2) MUTATED	65	11	6	17	6
DEL PEAK 31(13Q14.2) WILD-TYPE	99	69	100	116	41

Figure S850. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S851. Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 31(13Q14.2) MUTATED	32	59	14
DEL PEAK 31(13Q14.2) WILD-TYPE	186	113	126

Figure S851. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.026

Table S852. Gene #81: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 31(13Q14.2) MUTATED	39	18	20	16
DEL PEAK 31(13Q14.2) WILD-TYPE	77	80	72	76

Figure S852. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.019

Table S853. Gene #81: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 31(13Q14.2) MUTATED	47	20	26
DEL PEAK 31(13Q14.2) WILD-TYPE	116	112	77

Figure S853. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.01

Table S854. Gene #82: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 32(14Q13.1) MUTATED	0	5	0	0
DEL PEAK 32(14Q13.1) WILD-TYPE	15	12	14	7

Figure S854. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0052 (Fisher's exact test), Q value = 0.0065

Table S855. Gene #82: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 32(14Q13.1) MUTATED	1	4	0	0	0
DEL PEAK 32(14Q13.1) WILD-TYPE	13	5	7	7	16

Figure S855. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S856. Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 32(14Q13.1) MUTATED	69	2	0	2
DEL PEAK 32(14Q13.1) WILD-TYPE	139	176	99	52

Figure S856. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S857. Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 32(14Q13.1) MUTATED	44	15	5
DEL PEAK 32(14Q13.1) WILD-TYPE	110	63	188

Figure S857. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q13.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S858. Gene #82: 'del_14q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 32(14Q13.1) MUTATED	1	1	3	7	23	9	11
DEL PEAK 32(14Q13.1) WILD-TYPE	38	80	49	49	61	59	42

Figure S858. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S859. Gene #82: 'del_14q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 32(14Q13.1) MUTATED	1	39	8	7
DEL PEAK 32(14Q13.1) WILD-TYPE	107	143	85	43

Figure S859. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S860. Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 32(14Q13.1) MUTATED	57	4	5	6
DEL PEAK 32(14Q13.1) WILD-TYPE	131	119	88	127

Figure S860. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S861. Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 32(14Q13.1) MUTATED	50	1	5	1	9	5	1
DEL PEAK 32(14Q13.1) WILD-TYPE	73	52	42	64	99	61	74

Figure S861. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S862. Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 32(14Q13.1) MUTATED	50	6	6	4	6
DEL PEAK 32(14Q13.1) WILD-TYPE	114	74	100	129	41

Figure S862. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S863. Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 32(14Q13.1) MUTATED	14	54	4
DEL PEAK 32(14Q13.1) WILD-TYPE	204	118	136

Figure S863. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.00091

Table S864. Gene #82: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 32(14Q13.1) MUTATED	29	5	16	14
DEL PEAK 32(14Q13.1) WILD-TYPE	87	93	76	78

Figure S864. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00029

Table S865. Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 32(14Q13.1) MUTATED	38	8	18
DEL PEAK 32(14Q13.1) WILD-TYPE	125	124	85

Figure S865. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'MRNA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.049

Table S866. Gene #83: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 33(15Q15.1) MUTATED	1	5	0	0
DEL PEAK 33(15Q15.1) WILD-TYPE	14	12	14	7

Figure S866. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.013

Table S867. Gene #83: 'del_15q15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 33(15Q15.1) MUTATED	1	4	0	1	0
DEL PEAK 33(15Q15.1) WILD-TYPE	13	5	7	6	16

Figure S867. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S868. Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 33(15Q15.1) MUTATED	133	1	2	4
DEL PEAK 33(15Q15.1) WILD-TYPE	75	177	97	50

Figure S868. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S869. Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 33(15Q15.1) MUTATED	76	35	14
DEL PEAK 33(15Q15.1) WILD-TYPE	78	43	179

Figure S869. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S870. Gene #83: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 33(15Q15.1) MUTATED	6	2	7	22	38	16	20
DEL PEAK 33(15Q15.1) WILD-TYPE	33	79	45	34	46	52	33

Figure S870. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S871. Gene #83: 'del_15q15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 33(15Q15.1) MUTATED	6	71	23	11
DEL PEAK 33(15Q15.1) WILD-TYPE	102	111	70	39

Figure S871. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S872. Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 33(15Q15.1) MUTATED	112	10	9	9
DEL PEAK 33(15Q15.1) WILD-TYPE	76	113	84	124

Figure S872. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S873. Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 33(15Q15.1) MUTATED	86	1	14	4	25	9	1
DEL PEAK 33(15Q15.1) WILD-TYPE	37	52	33	61	83	57	74

Figure S873. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S874. Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 33(15Q15.1) MUTATED	98	8	6	11	15
DEL PEAK 33(15Q15.1) WILD-TYPE	66	72	100	122	32

Figure S874. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S875. Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 33(15Q15.1) MUTATED	35	94	9
DEL PEAK 33(15Q15.1) WILD-TYPE	183	78	131

Figure S875. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S876. Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 33(15Q15.1) MUTATED	60	11	29	22
DEL PEAK 33(15Q15.1) WILD-TYPE	56	87	63	70

Figure S876. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S877. Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 33(15Q15.1) MUTATED	68	16	38
DEL PEAK 33(15Q15.1) WILD-TYPE	95	116	65

Figure S877. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q23' versus 'MRNA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0033

Table S878. Gene #84: 'del_15q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 34(15Q23) MUTATED	0	6	0	0
DEL PEAK 34(15Q23) WILD-TYPE	15	11	14	7

Figure S878. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.00072

Table S879. Gene #84: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 34(15Q23) MUTATED	1	5	0	0	0
DEL PEAK 34(15Q23) WILD-TYPE	13	4	7	7	16

Figure S879. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S880. Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 34(15Q23) MUTATED	110	0	2	3
DEL PEAK 34(15Q23) WILD-TYPE	98	178	97	51

Figure S880. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S881. Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 34(15Q23) MUTATED	67	24	10
DEL PEAK 34(15Q23) WILD-TYPE	87	54	183

Figure S881. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S882. Gene #84: 'del_15q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 34(15Q23) MUTATED	4	3	7	15	33	15	14
DEL PEAK 34(15Q23) WILD-TYPE	35	78	45	41	51	53	39

Figure S882. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S883. Gene #84: 'del_15q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 34(15Q23) MUTATED	4	57	20	10
DEL PEAK 34(15Q23) WILD-TYPE	104	125	73	40

Figure S883. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S884. Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 34(15Q23) MUTATED	92	11	6	6
DEL PEAK 34(15Q23) WILD-TYPE	96	112	87	127

Figure S884. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S885. Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 34(15Q23) MUTATED	75	1	12	2	17	7	1
DEL PEAK 34(15Q23) WILD-TYPE	48	52	35	63	91	59	74

Figure S885. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S886. Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 34(15Q23) MUTATED	81	8	4	9	11
DEL PEAK 34(15Q23) WILD-TYPE	83	72	102	124	36

Figure S886. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S887. Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 34(15Q23) MUTATED	30	77	6
DEL PEAK 34(15Q23) WILD-TYPE	188	95	134

Figure S887. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S888. Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 34(15Q23) MUTATED	51	8	20	19
DEL PEAK 34(15Q23) WILD-TYPE	65	90	72	73

Figure S888. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S889. Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 34(15Q23) MUTATED	60	9	29
DEL PEAK 34(15Q23) WILD-TYPE	103	123	74

Figure S889. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'MRNA_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.013

Table S890. Gene #85: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 35(16P13.3) MUTATED	1	6	0	0
DEL PEAK 35(16P13.3) WILD-TYPE	14	11	14	7

Figure S890. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00968 (Fisher's exact test), Q value = 0.012

Table S891. Gene #85: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 35(16P13.3) MUTATED	3	4	0	0	0
DEL PEAK 35(16P13.3) WILD-TYPE	11	5	7	7	16

Figure S891. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S892. Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 35(16P13.3) MUTATED	90	0	1	1
DEL PEAK 35(16P13.3) WILD-TYPE	118	178	98	53

Figure S892. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S893. Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 35(16P13.3) MUTATED	52	26	5
DEL PEAK 35(16P13.3) WILD-TYPE	102	52	188

Figure S893. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S894. Gene #85: 'del_16p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 35(16P13.3) MUTATED	2	2	4	15	29	11	13
DEL PEAK 35(16P13.3) WILD-TYPE	37	79	48	41	55	57	40

Figure S894. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S895. Gene #85: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 35(16P13.3) MUTATED	1	53	15	7
DEL PEAK 35(16P13.3) WILD-TYPE	107	129	78	43

Figure S895. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S896. Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 35(16P13.3) MUTATED	79	4	2	7
DEL PEAK 35(16P13.3) WILD-TYPE	109	119	91	126

Figure S896. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S897. Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 35(16P13.3) MUTATED	63	1	9	1	11	6	1
DEL PEAK 35(16P13.3) WILD-TYPE	60	52	38	64	97	60	74

Figure S897. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S898. Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 35(16P13.3) MUTATED	66	4	5	7	8
DEL PEAK 35(16P13.3) WILD-TYPE	98	76	101	126	39

Figure S898. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S899. Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 35(16P13.3) MUTATED	17	68	5
DEL PEAK 35(16P13.3) WILD-TYPE	201	104	135

Figure S899. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S900. Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 35(16P13.3) MUTATED	43	8	18	13
DEL PEAK 35(16P13.3) WILD-TYPE	73	90	74	79

Figure S900. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S901. Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 35(16P13.3) MUTATED	48	8	26
DEL PEAK 35(16P13.3) WILD-TYPE	115	124	77

Figure S901. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNA_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0014

Table S902. Gene #86: 'del_16q21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 36(16Q21) MUTATED	0	8	1	0
DEL PEAK 36(16Q21) WILD-TYPE	15	9	13	7

Figure S902. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q21' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S903. Gene #86: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 36(16Q21) MUTATED	1	7	0	0	1
DEL PEAK 36(16Q21) WILD-TYPE	13	2	7	7	15

Figure S903. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S904. Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 36(16Q21) MUTATED	139	3	9	3
DEL PEAK 36(16Q21) WILD-TYPE	69	175	90	51

Figure S904. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S905. Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 36(16Q21) MUTATED	80	37	18
DEL PEAK 36(16Q21) WILD-TYPE	74	41	175

Figure S905. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S906. Gene #86: 'del_16q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 36(16Q21) MUTATED	4	7	10	22	45	18	18
DEL PEAK 36(16Q21) WILD-TYPE	35	74	42	34	39	50	35

Figure S906. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S907. Gene #86: 'del_16q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 36(16Q21) MUTATED	10	81	22	11
DEL PEAK 36(16Q21) WILD-TYPE	98	101	71	39

Figure S907. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S908. Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 36(16Q21) MUTATED	113	15	11	14
DEL PEAK 36(16Q21) WILD-TYPE	75	108	82	119

Figure S908. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S909. Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 36(16Q21) MUTATED	89	7	17	3	22	11	4
DEL PEAK 36(16Q21) WILD-TYPE	34	46	30	62	86	55	71

Figure S909. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S910. Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 36(16Q21) MUTATED	96	13	13	15	13
DEL PEAK 36(16Q21) WILD-TYPE	68	67	93	118	34

Figure S910. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S911. Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 36(16Q21) MUTATED	38	98	14
DEL PEAK 36(16Q21) WILD-TYPE	180	74	126

Figure S911. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S912. Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 36(16Q21) MUTATED	55	16	29	31
DEL PEAK 36(16Q21) WILD-TYPE	61	82	63	61

Figure S912. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S913. Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 36(16Q21) MUTATED	70	22	39
DEL PEAK 36(16Q21) WILD-TYPE	93	110	64

Figure S913. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.012

Table S914. Gene #87: 'del_16q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 37(16Q22.3) MUTATED	4	5	0	0	1
DEL PEAK 37(16Q22.3) WILD-TYPE	10	4	7	7	15

Figure S914. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S915. Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 37(16Q22.3) MUTATED	140	3	12	3
DEL PEAK 37(16Q22.3) WILD-TYPE	68	175	87	51

Figure S915. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S916. Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 37(16Q22.3) MUTATED	78	39	21
DEL PEAK 37(16Q22.3) WILD-TYPE	76	39	172

Figure S916. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q22.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S917. Gene #87: 'del_16q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 37(16Q22.3) MUTATED	5	7	9	27	42	17	16
DEL PEAK 37(16Q22.3) WILD-TYPE	34	74	43	29	42	51	37

Figure S917. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S918. Gene #87: 'del_16q22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 37(16Q22.3) MUTATED	13	78	22	10
DEL PEAK 37(16Q22.3) WILD-TYPE	95	104	71	40

Figure S918. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S919. Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 37(16Q22.3) MUTATED	114	16	12	16
DEL PEAK 37(16Q22.3) WILD-TYPE	74	107	81	117

Figure S919. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S920. Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 37(16Q22.3) MUTATED	88	8	18	3	24	12	5
DEL PEAK 37(16Q22.3) WILD-TYPE	35	45	29	62	84	54	70

Figure S920. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S921. Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 37(16Q22.3) MUTATED	94	14	14	17	15
DEL PEAK 37(16Q22.3) WILD-TYPE	70	66	92	116	32

Figure S921. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S922. Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 37(16Q22.3) MUTATED	39	99	16
DEL PEAK 37(16Q22.3) WILD-TYPE	179	73	124

Figure S922. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S923. Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 37(16Q22.3) MUTATED	55	17	31	31
DEL PEAK 37(16Q22.3) WILD-TYPE	61	81	61	61

Figure S923. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S924. Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 37(16Q22.3) MUTATED	69	22	43
DEL PEAK 37(16Q22.3) WILD-TYPE	94	110	60

Figure S924. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.00484 (Fisher's exact test), Q value = 0.006

Table S925. Gene #88: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 38(16Q23.1) MUTATED	1	9	2	0
DEL PEAK 38(16Q23.1) WILD-TYPE	14	8	12	7

Figure S925. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00027

Table S926. Gene #88: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 38(16Q23.1) MUTATED	4	7	0	0	1
DEL PEAK 38(16Q23.1) WILD-TYPE	10	2	7	7	15

Figure S926. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S927. Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 38(16Q23.1) MUTATED	147	4	12	3
DEL PEAK 38(16Q23.1) WILD-TYPE	61	174	87	51

Figure S927. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S928. Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 38(16Q23.1) MUTATED	84	37	21
DEL PEAK 38(16Q23.1) WILD-TYPE	70	41	172

Figure S928. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S929. Gene #88: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 38(16Q23.1) MUTATED	5	7	10	28	45	19	18
DEL PEAK 38(16Q23.1) WILD-TYPE	34	74	42	28	39	49	35

Figure S929. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S930. Gene #88: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 38(16Q23.1) MUTATED	13	84	23	12
DEL PEAK 38(16Q23.1) WILD-TYPE	95	98	70	38

Figure S930. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S931. Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 38(16Q23.1) MUTATED	120	16	15	15
DEL PEAK 38(16Q23.1) WILD-TYPE	68	107	78	118

Figure S931. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S932. Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 38(16Q23.1) MUTATED	93	8	20	4	25	11	5
DEL PEAK 38(16Q23.1) WILD-TYPE	30	45	27	61	83	55	70

Figure S932. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S933. Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 38(16Q23.1) MUTATED	100	14	16	16	15
DEL PEAK 38(16Q23.1) WILD-TYPE	64	66	90	117	32

Figure S933. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S934. Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 38(16Q23.1) MUTATED	38	108	15
DEL PEAK 38(16Q23.1) WILD-TYPE	180	64	125

Figure S934. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S935. Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 38(16Q23.1) MUTATED	59	16	32	31
DEL PEAK 38(16Q23.1) WILD-TYPE	57	82	60	61

Figure S935. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S936. Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 38(16Q23.1) MUTATED	73	21	44
DEL PEAK 38(16Q23.1) WILD-TYPE	90	111	59

Figure S936. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'MRNA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.00097

Table S937. Gene #89: 'del_17p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 39(17P13.3) MUTATED	0	8	1	0
DEL PEAK 39(17P13.3) WILD-TYPE	15	9	13	7

Figure S937. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S938. Gene #89: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 39(17P13.3) MUTATED	1	7	1	0	0
DEL PEAK 39(17P13.3) WILD-TYPE	13	2	6	7	16

Figure S938. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S939. Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 39(17P13.3) MUTATED	116	1	3	2
DEL PEAK 39(17P13.3) WILD-TYPE	92	177	96	52

Figure S939. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S940. Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 39(17P13.3) MUTATED	62	26	16
DEL PEAK 39(17P13.3) WILD-TYPE	92	52	177

Figure S940. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S941. Gene #89: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 39(17P13.3) MUTATED	4	2	6	17	37	14	17
DEL PEAK 39(17P13.3) WILD-TYPE	35	79	46	39	47	54	36

Figure S941. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S942. Gene #89: 'del_17p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 39(17P13.3) MUTATED	4	62	21	10
DEL PEAK 39(17P13.3) WILD-TYPE	104	120	72	40

Figure S942. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S943. Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 39(17P13.3) MUTATED	94	8	6	13
DEL PEAK 39(17P13.3) WILD-TYPE	94	115	87	120

Figure S943. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S944. Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 39(17P13.3) MUTATED	79	1	8	3	16	13	1
DEL PEAK 39(17P13.3) WILD-TYPE	44	52	39	62	92	53	74

Figure S944. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S945. Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 39(17P13.3) MUTATED	81	8	8	13	9
DEL PEAK 39(17P13.3) WILD-TYPE	83	72	98	120	38

Figure S945. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S946. Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 39(17P13.3) MUTATED	32	75	12
DEL PEAK 39(17P13.3) WILD-TYPE	186	97	128

Figure S946. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S947. Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 39(17P13.3) MUTATED	50	13	23	14
DEL PEAK 39(17P13.3) WILD-TYPE	66	85	69	78

Figure S947. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0016

Table S948. Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 39(17P13.3) MUTATED	52	19	29
DEL PEAK 39(17P13.3) WILD-TYPE	111	113	74

Figure S948. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0012

Table S949. Gene #90: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 40(17P11.2) MUTATED	0	8	1	0
DEL PEAK 40(17P11.2) WILD-TYPE	15	9	13	7

Figure S949. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S950. Gene #90: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 40(17P11.2) MUTATED	0	8	1	0	0
DEL PEAK 40(17P11.2) WILD-TYPE	14	1	6	7	16

Figure S950. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S951. Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 40(17P11.2) MUTATED	122	2	2	2
DEL PEAK 40(17P11.2) WILD-TYPE	86	176	97	52

Figure S951. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S952. Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 40(17P11.2) MUTATED	67	31	14
DEL PEAK 40(17P11.2) WILD-TYPE	87	47	179

Figure S952. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S953. Gene #90: 'del_17p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 40(17P11.2) MUTATED	4	2	5	14	39	14	18
DEL PEAK 40(17P11.2) WILD-TYPE	35	79	47	42	45	54	35

Figure S953. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S954. Gene #90: 'del_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 40(17P11.2) MUTATED	4	64	17	11
DEL PEAK 40(17P11.2) WILD-TYPE	104	118	76	39

Figure S954. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S955. Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 40(17P11.2) MUTATED	100	6	10	12
DEL PEAK 40(17P11.2) WILD-TYPE	88	117	83	121

Figure S955. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S956. Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 40(17P11.2) MUTATED	85	1	10	2	17	12	1
DEL PEAK 40(17P11.2) WILD-TYPE	38	52	37	63	91	54	74

Figure S956. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S957. Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 40(17P11.2) MUTATED	85	6	8	14	11
DEL PEAK 40(17P11.2) WILD-TYPE	79	74	98	119	36

Figure S957. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S958. Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 40(17P11.2) MUTATED	27	84	13
DEL PEAK 40(17P11.2) WILD-TYPE	191	88	127

Figure S958. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S959. Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 40(17P11.2) MUTATED	50	13	25	19
DEL PEAK 40(17P11.2) WILD-TYPE	66	85	67	73

Figure S959. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00018

Table S960. Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 40(17P11.2) MUTATED	55	18	34
DEL PEAK 40(17P11.2) WILD-TYPE	108	114	69

Figure S960. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00073

Table S961. Gene #91: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 41(17Q11.2) MUTATED	0	7	0	0
DEL PEAK 41(17Q11.2) WILD-TYPE	15	10	14	7

Figure S961. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S962. Gene #91: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 41(17Q11.2) MUTATED	0	7	0	0	0
DEL PEAK 41(17Q11.2) WILD-TYPE	14	2	7	7	16

Figure S962. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S963. Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 41(17Q11.2) MUTATED	101	1	1	2
DEL PEAK 41(17Q11.2) WILD-TYPE	107	177	98	52

Figure S963. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S964. Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 41(17Q11.2) MUTATED	48	26	16
DEL PEAK 41(17Q11.2) WILD-TYPE	106	52	177

Figure S964. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S965. Gene #91: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 41(17Q11.2) MUTATED	4	3	6	15	27	11	14
DEL PEAK 41(17Q11.2) WILD-TYPE	35	78	46	41	57	57	39

Figure S965. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S966. Gene #91: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 41(17Q11.2) MUTATED	4	52	16	8
DEL PEAK 41(17Q11.2) WILD-TYPE	104	130	77	42

Figure S966. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S967. Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 41(17Q11.2) MUTATED	78	8	6	12
DEL PEAK 41(17Q11.2) WILD-TYPE	110	115	87	121

Figure S967. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S968. Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 41(17Q11.2) MUTATED	62	1	6	3	19	11	2
DEL PEAK 41(17Q11.2) WILD-TYPE	61	52	41	62	89	55	73

Figure S968. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S969. Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 41(17Q11.2) MUTATED	66	6	7	14	8
DEL PEAK 41(17Q11.2) WILD-TYPE	98	74	99	119	39

Figure S969. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S970. Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 41(17Q11.2) MUTATED	28	60	13
DEL PEAK 41(17Q11.2) WILD-TYPE	190	112	127

Figure S970. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00231 (Fisher's exact test), Q value = 0.003

Table S971. Gene #91: 'del_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 41(17Q11.2) MUTATED	38	11	20	19
DEL PEAK 41(17Q11.2) WILD-TYPE	78	87	72	73

Figure S971. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.031

Table S972. Gene #91: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 41(17Q11.2) MUTATED	43	19	26
DEL PEAK 41(17Q11.2) WILD-TYPE	120	113	77

Figure S972. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S973. Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 42(17Q21.31) MUTATED	0	9	0	0
DEL PEAK 42(17Q21.31) WILD-TYPE	15	8	14	7

Figure S973. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S974. Gene #92: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 42(17Q21.31) MUTATED	1	8	0	0	0
DEL PEAK 42(17Q21.31) WILD-TYPE	13	1	7	7	16

Figure S974. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S975. Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 42(17Q21.31) MUTATED	111	0	1	2
DEL PEAK 42(17Q21.31) WILD-TYPE	97	178	98	52

Figure S975. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S976. Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 42(17Q21.31) MUTATED	50	33	16
DEL PEAK 42(17Q21.31) WILD-TYPE	104	45	177

Figure S976. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S977. Gene #92: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 42(17Q21.31) MUTATED	3	3	8	17	32	12	13
DEL PEAK 42(17Q21.31) WILD-TYPE	36	78	44	39	52	56	40

Figure S977. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S978. Gene #92: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 42(17Q21.31) MUTATED	3	59	19	7
DEL PEAK 42(17Q21.31) WILD-TYPE	105	123	74	43

Figure S978. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S979. Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 42(17Q21.31) MUTATED	88	7	5	13
DEL PEAK 42(17Q21.31) WILD-TYPE	100	116	88	120

Figure S979. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S980. Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 42(17Q21.31) MUTATED	72	1	6	3	18	12	1
DEL PEAK 42(17Q21.31) WILD-TYPE	51	52	41	62	90	54	74

Figure S980. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S981. Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 42(17Q21.31) MUTATED	73	7	7	15	7
DEL PEAK 42(17Q21.31) WILD-TYPE	91	73	99	118	40

Figure S981. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S982. Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 42(17Q21.31) MUTATED	29	66	14
DEL PEAK 42(17Q21.31) WILD-TYPE	189	106	126

Figure S982. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S983. Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 42(17Q21.31) MUTATED	46	16	18	16
DEL PEAK 42(17Q21.31) WILD-TYPE	70	82	74	76

Figure S983. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.018

Table S984. Gene #92: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 42(17Q21.31) MUTATED	49	21	26
DEL PEAK 42(17Q21.31) WILD-TYPE	114	111	77

Figure S984. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S985. Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 43(18Q21.2) MUTATED	87	0	2	1
DEL PEAK 43(18Q21.2) WILD-TYPE	121	178	97	53

Figure S985. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S986. Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 43(18Q21.2) MUTATED	47	21	12
DEL PEAK 43(18Q21.2) WILD-TYPE	107	57	181

Figure S986. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S987. Gene #93: 'del_18q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 43(18Q21.2) MUTATED	3	3	6	18	26	9	12
DEL PEAK 43(18Q21.2) WILD-TYPE	36	78	46	38	58	59	41

Figure S987. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S988. Gene #93: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 43(18Q21.2) MUTATED	4	47	18	8
DEL PEAK 43(18Q21.2) WILD-TYPE	104	135	75	42

Figure S988. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S989. Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 43(18Q21.2) MUTATED	64	7	11	8
DEL PEAK 43(18Q21.2) WILD-TYPE	124	116	82	125

Figure S989. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S990. Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 43(18Q21.2) MUTATED	41	1	15	1	24	8	0
DEL PEAK 43(18Q21.2) WILD-TYPE	82	52	32	64	84	58	75

Figure S990. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S991. Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 43(18Q21.2) MUTATED	57	5	7	11	9
DEL PEAK 43(18Q21.2) WILD-TYPE	107	75	99	122	38

Figure S991. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S992. Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 43(18Q21.2) MUTATED	24	57	8
DEL PEAK 43(18Q21.2) WILD-TYPE	194	115	132

Figure S992. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 6e-04

Table S993. Gene #93: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 43(18Q21.2) MUTATED	36	8	17	17
DEL PEAK 43(18Q21.2) WILD-TYPE	80	90	75	75

Figure S993. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0019

Table S994. Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 43(18Q21.2) MUTATED	44	14	20
DEL PEAK 43(18Q21.2) WILD-TYPE	119	118	83

Figure S994. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S995. Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 44(18Q23) MUTATED	95	1	2	0
DEL PEAK 44(18Q23) WILD-TYPE	113	177	97	54

Figure S995. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S996. Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 44(18Q23) MUTATED	54	20	12
DEL PEAK 44(18Q23) WILD-TYPE	100	58	181

Figure S996. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S997. Gene #94: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 44(18Q23) MUTATED	4	3	7	18	28	12	11
DEL PEAK 44(18Q23) WILD-TYPE	35	78	45	38	56	56	42

Figure S997. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S998. Gene #94: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 44(18Q23) MUTATED	5	54	19	5
DEL PEAK 44(18Q23) WILD-TYPE	103	128	74	45

Figure S998. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S999. Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 44(18Q23) MUTATED	70	9	10	9
DEL PEAK 44(18Q23) WILD-TYPE	118	114	83	124

Figure S999. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1000. Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 44(18Q23) MUTATED	46	1	19	1	22	8	1
DEL PEAK 44(18Q23) WILD-TYPE	77	52	28	64	86	58	74

Figure S1000. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1001. Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 44(18Q23) MUTATED	61	6	7	12	10
DEL PEAK 44(18Q23) WILD-TYPE	103	74	99	121	37

Figure S1001. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1002. Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 44(18Q23) MUTATED	25	62	9
DEL PEAK 44(18Q23) WILD-TYPE	193	110	131

Figure S1002. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S1003. Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 44(18Q23) MUTATED	38	8	21	17
DEL PEAK 44(18Q23) WILD-TYPE	78	90	71	75

Figure S1003. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.0023

Table S1004. Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 44(18Q23) MUTATED	45	15	24
DEL PEAK 44(18Q23) WILD-TYPE	118	117	79

Figure S1004. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S1005. Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 45(19P13.3) MUTATED	1	11	0	0
DEL PEAK 45(19P13.3) WILD-TYPE	14	6	14	7

Figure S1005. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1006. Gene #95: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 45(19P13.3) MUTATED	3	9	0	0	0
DEL PEAK 45(19P13.3) WILD-TYPE	11	0	7	7	16

Figure S1006. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1007. Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 45(19P13.3) MUTATED	155	0	0	2
DEL PEAK 45(19P13.3) WILD-TYPE	53	178	99	52

Figure S1007. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1008. Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 45(19P13.3) MUTATED	93	37	7
DEL PEAK 45(19P13.3) WILD-TYPE	61	41	186

Figure S1008. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1009. Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 45(19P13.3) MUTATED	2	3	9	26	47	17	19
DEL PEAK 45(19P13.3) WILD-TYPE	37	78	43	30	37	51	34

Figure S1009. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1010. Gene #95: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 45(19P13.3) MUTATED	2	87	23	11
DEL PEAK 45(19P13.3) WILD-TYPE	106	95	70	39

Figure S1010. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1011. Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 45(19P13.3) MUTATED	132	5	11	8
DEL PEAK 45(19P13.3) WILD-TYPE	56	118	82	125

Figure S1011. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1012. Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 45(19P13.3) MUTATED	105	1	20	2	21	7	0
DEL PEAK 45(19P13.3) WILD-TYPE	18	52	27	63	87	59	75

Figure S1012. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1013. Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 45(19P13.3) MUTATED	114	5	10	10	13
DEL PEAK 45(19P13.3) WILD-TYPE	50	75	96	123	34

Figure S1013. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1014. Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 45(19P13.3) MUTATED	27	115	10
DEL PEAK 45(19P13.3) WILD-TYPE	191	57	130

Figure S1014. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1015. Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 45(19P13.3) MUTATED	62	11	28	31
DEL PEAK 45(19P13.3) WILD-TYPE	54	87	64	61

Figure S1015. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1016. Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 45(19P13.3) MUTATED	78	15	39
DEL PEAK 45(19P13.3) WILD-TYPE	85	117	64

Figure S1016. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1017. Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 46(19P12) MUTATED	55	1	0	2
DEL PEAK 46(19P12) WILD-TYPE	153	177	99	52

Figure S1017. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1018. Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 46(19P12) MUTATED	33	14	5
DEL PEAK 46(19P12) WILD-TYPE	121	64	188

Figure S1018. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p12' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0016

Table S1019. Gene #96: 'del_19p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 46(19P12) MUTATED	2	2	5	9	19	7	3
DEL PEAK 46(19P12) WILD-TYPE	37	79	47	47	65	61	50

Figure S1019. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p12' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S1020. Gene #96: 'del_19p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 46(19P12) MUTATED	2	32	12	1
DEL PEAK 46(19P12) WILD-TYPE	106	150	81	49

Figure S1020. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1021. Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 46(19P12) MUTATED	42	4	6	6
DEL PEAK 46(19P12) WILD-TYPE	146	119	87	127

Figure S1021. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1022. Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 46(19P12) MUTATED	32	1	9	1	11	4	0
DEL PEAK 46(19P12) WILD-TYPE	91	52	38	64	97	62	75

Figure S1022. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1023. Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 46(19P12) MUTATED	38	5	4	5	5
DEL PEAK 46(19P12) WILD-TYPE	126	75	102	128	42

Figure S1023. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1024. Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 46(19P12) MUTATED	17	36	4
DEL PEAK 46(19P12) WILD-TYPE	201	136	136

Figure S1024. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00586 (Fisher's exact test), Q value = 0.0072

Table S1025. Gene #96: 'del_19p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 46(19P12) MUTATED	24	6	7	13
DEL PEAK 46(19P12) WILD-TYPE	92	92	85	79

Figure S1025. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00029

Table S1026. Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 46(19P12) MUTATED	33	6	11
DEL PEAK 46(19P12) WILD-TYPE	130	126	92

Figure S1026. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0012

Table S1027. Gene #97: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 47(19Q13.43) MUTATED	0	8	1	0
DEL PEAK 47(19Q13.43) WILD-TYPE	15	9	13	7

Figure S1027. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1028. Gene #97: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 47(19Q13.43) MUTATED	1	7	1	0	0
DEL PEAK 47(19Q13.43) WILD-TYPE	13	2	6	7	16

Figure S1028. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1029. Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 47(19Q13.43) MUTATED	65	0	1	1
DEL PEAK 47(19Q13.43) WILD-TYPE	143	178	98	53

Figure S1029. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1030. Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 47(19Q13.43) MUTATED	38	16	2
DEL PEAK 47(19Q13.43) WILD-TYPE	116	62	191

Figure S1030. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.43' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1031. Gene #97: 'del_19q13.43' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 47(19Q13.43) MUTATED	1	0	4	11	18	6	10
DEL PEAK 47(19Q13.43) WILD-TYPE	38	81	48	45	66	62	43

Figure S1031. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.43' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S1032. Gene #97: 'del_19q13.43' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 47(19Q13.43) MUTATED	1	34	11	4
DEL PEAK 47(19Q13.43) WILD-TYPE	107	148	82	46

Figure S1032. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1033. Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 47(19Q13.43) MUTATED	54	3	6	3
DEL PEAK 47(19Q13.43) WILD-TYPE	134	120	87	130

Figure S1033. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1034. Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 47(19Q13.43) MUTATED	44	1	8	0	11	2	0
DEL PEAK 47(19Q13.43) WILD-TYPE	79	52	39	65	97	64	75

Figure S1034. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1035. Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 47(19Q13.43) MUTATED	47	3	5	4	4
DEL PEAK 47(19Q13.43) WILD-TYPE	117	77	101	129	43

Figure S1035. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1036. Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 47(19Q13.43) MUTATED	11	50	2
DEL PEAK 47(19Q13.43) WILD-TYPE	207	122	138

Figure S1036. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.0045

Table S1037. Gene #97: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 47(19Q13.43) MUTATED	22	4	14	16
DEL PEAK 47(19Q13.43) WILD-TYPE	94	94	78	76

Figure S1037. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S1038. Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 47(19Q13.43) MUTATED	31	4	21
DEL PEAK 47(19Q13.43) WILD-TYPE	132	128	82

Figure S1038. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1039. Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 48(20P12.1) MUTATED	28	2	2	3
DEL PEAK 48(20P12.1) WILD-TYPE	180	176	97	51

Figure S1039. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.023

Table S1040. Gene #98: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 48(20P12.1) MUTATED	14	8	6
DEL PEAK 48(20P12.1) WILD-TYPE	140	70	187

Figure S1040. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0041 (Fisher's exact test), Q value = 0.0052

Table S1041. Gene #98: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 48(20P12.1) MUTATED	5	21	1	2
DEL PEAK 48(20P12.1) WILD-TYPE	103	161	92	48

Figure S1041. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00822 (Fisher's exact test), Q value = 0.01

Table S1042. Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 48(20P12.1) MUTATED	22	4	3	6
DEL PEAK 48(20P12.1) WILD-TYPE	166	119	90	127

Figure S1042. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.0033

Table S1043. Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 48(20P12.1) MUTATED	17	3	5	0	6	2	2
DEL PEAK 48(20P12.1) WILD-TYPE	106	50	42	65	102	64	73

Figure S1043. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00026

Table S1044. Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 48(20P12.1) MUTATED	23	4	2	3	2
DEL PEAK 48(20P12.1) WILD-TYPE	141	76	104	130	45

Figure S1044. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00536 (Fisher's exact test), Q value = 0.0066

Table S1045. Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 48(20P12.1) MUTATED	8	20	6
DEL PEAK 48(20P12.1) WILD-TYPE	210	152	134

Figure S1045. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.05

Table S1046. Gene #98: 'del_20p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 48(20P12.1) MUTATED	15	3	6	5
DEL PEAK 48(20P12.1) WILD-TYPE	101	95	86	87

Figure S1046. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q12.1' versus 'MRNA_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.0032

Table S1047. Gene #99: 'del_22q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 49(22Q12.1) MUTATED	0	6	0	0
DEL PEAK 49(22Q12.1) WILD-TYPE	15	11	14	7

Figure S1047. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00738 (Fisher's exact test), Q value = 0.009

Table S1048. Gene #99: 'del_22q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 49(22Q12.1) MUTATED	2	4	0	0	0
DEL PEAK 49(22Q12.1) WILD-TYPE	12	5	7	7	16

Figure S1048. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1049. Gene #99: 'del_22q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 49(22Q12.1) MUTATED	90	2	2	1
DEL PEAK 49(22Q12.1) WILD-TYPE	118	176	97	53

Figure S1049. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1050. Gene #99: 'del_22q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 49(22Q12.1) MUTATED	47	20	17
DEL PEAK 49(22Q12.1) WILD-TYPE	107	58	176

Figure S1050. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q12.1' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.00079

Table S1051. Gene #99: 'del_22q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 49(22Q12.1) MUTATED	3	5	7	16	24	9	10
DEL PEAK 49(22Q12.1) WILD-TYPE	36	76	45	40	60	59	43

Figure S1051. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S1052. Gene #99: 'del_22q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 49(22Q12.1) MUTATED	3	45	19	7
DEL PEAK 49(22Q12.1) WILD-TYPE	105	137	74	43

Figure S1052. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1053. Gene #99: 'del_22q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 49(22Q12.1) MUTATED	66	9	6	14
DEL PEAK 49(22Q12.1) WILD-TYPE	122	114	87	119

Figure S1053. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1054. Gene #99: 'del_22q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 49(22Q12.1) MUTATED	49	1	4	1	24	15	1
DEL PEAK 49(22Q12.1) WILD-TYPE	74	52	43	64	84	51	74

Figure S1054. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1055. Gene #99: 'del_22q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 49(22Q12.1) MUTATED	61	6	2	18	6
DEL PEAK 49(22Q12.1) WILD-TYPE	103	74	104	115	41

Figure S1055. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.7e-05

Table S1056. Gene #99: 'del_22q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 49(22Q12.1) MUTATED	29	49	15
DEL PEAK 49(22Q12.1) WILD-TYPE	189	123	125

Figure S1056. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00794 (Fisher's exact test), Q value = 0.0097

Table S1057. Gene #99: 'del_22q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 49(22Q12.1) MUTATED	34	16	19	10
DEL PEAK 49(22Q12.1) WILD-TYPE	82	82	73	82

Figure S1057. Get High-res Image Gene #99: 'del_22q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 9.1e-05

Table S1058. Gene #100: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 50(22Q13.32) MUTATED	0	9	0	0
DEL PEAK 50(22Q13.32) WILD-TYPE	15	8	14	7

Figure S1058. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S1059. Gene #100: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 50(22Q13.32) MUTATED	2	7	0	0	0
DEL PEAK 50(22Q13.32) WILD-TYPE	12	2	7	7	16

Figure S1059. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1060. Gene #100: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 50(22Q13.32) MUTATED	133	3	3	1
DEL PEAK 50(22Q13.32) WILD-TYPE	75	175	96	53

Figure S1060. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1061. Gene #100: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 50(22Q13.32) MUTATED	72	32	20
DEL PEAK 50(22Q13.32) WILD-TYPE	82	46	173

Figure S1061. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1062. Gene #100: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 50(22Q13.32) MUTATED	3	5	8	21	41	16	18
DEL PEAK 50(22Q13.32) WILD-TYPE	36	76	44	35	43	52	35

Figure S1062. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1063. Gene #100: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 50(22Q13.32) MUTATED	4	72	24	12
DEL PEAK 50(22Q13.32) WILD-TYPE	104	110	69	38

Figure S1063. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1064. Gene #100: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 50(22Q13.32) MUTATED	104	10	9	16
DEL PEAK 50(22Q13.32) WILD-TYPE	84	113	84	117

Figure S1064. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1065. Gene #100: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 50(22Q13.32) MUTATED	83	1	10	2	26	14	3
DEL PEAK 50(22Q13.32) WILD-TYPE	40	52	37	63	82	52	72

Figure S1065. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1066. Gene #100: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 50(22Q13.32) MUTATED	93	7	7	19	10
DEL PEAK 50(22Q13.32) WILD-TYPE	71	73	99	114	37

Figure S1066. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1067. Gene #100: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 50(22Q13.32) MUTATED	34	86	16
DEL PEAK 50(22Q13.32) WILD-TYPE	184	86	124

Figure S1067. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S1068. Gene #100: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 50(22Q13.32) MUTATED	53	18	24	23
DEL PEAK 50(22Q13.32) WILD-TYPE	63	80	68	69

Figure S1068. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1069. Gene #100: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 50(22Q13.32) MUTATED	65	20	33
DEL PEAK 50(22Q13.32) WILD-TYPE	98	112	70

Figure S1069. Get High-res Image Gene #100: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'MRNA_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00073

Table S1070. Gene #101: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
DEL PEAK 51(XP21.1) MUTATED	0	7	0	0
DEL PEAK 51(XP21.1) WILD-TYPE	15	10	14	7

Figure S1070. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xp21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0014

Table S1071. Gene #101: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 51(XP21.1) MUTATED	2	5	0	0	0
DEL PEAK 51(XP21.1) WILD-TYPE	12	4	7	7	16

Figure S1071. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1072. Gene #101: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
DEL PEAK 51(XP21.1) MUTATED	85	2	0	1
DEL PEAK 51(XP21.1) WILD-TYPE	123	176	99	53

Figure S1072. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1073. Gene #101: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
DEL PEAK 51(XP21.1) MUTATED	46	18	10
DEL PEAK 51(XP21.1) WILD-TYPE	108	60	183

Figure S1073. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1074. Gene #101: 'del_xp21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
DEL PEAK 51(XP21.1) MUTATED	2	2	6	14	30	8	12
DEL PEAK 51(XP21.1) WILD-TYPE	37	79	46	42	54	60	41

Figure S1074. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xp21.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1075. Gene #101: 'del_xp21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 51(XP21.1) MUTATED	4	51	13	6
DEL PEAK 51(XP21.1) WILD-TYPE	104	131	80	44

Figure S1075. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1076. Gene #101: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
DEL PEAK 51(XP21.1) MUTATED	70	6	5	6
DEL PEAK 51(XP21.1) WILD-TYPE	118	117	88	127

Figure S1076. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1077. Gene #101: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 51(XP21.1) MUTATED	56	2	10	1	14	4	0
DEL PEAK 51(XP21.1) WILD-TYPE	67	51	37	64	94	62	75

Figure S1077. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1078. Gene #101: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
DEL PEAK 51(XP21.1) MUTATED	61	4	6	8	6
DEL PEAK 51(XP21.1) WILD-TYPE	103	76	100	125	41

Figure S1078. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.7e-05

Table S1079. Gene #101: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
DEL PEAK 51(XP21.1) MUTATED	22	58	5
DEL PEAK 51(XP21.1) WILD-TYPE	196	114	135

Figure S1079. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6.2e-05

Table S1080. Gene #101: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
DEL PEAK 51(XP21.1) MUTATED	39	9	15	11
DEL PEAK 51(XP21.1) WILD-TYPE	77	89	77	81

Figure S1080. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.2e-05

Table S1081. Gene #101: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
DEL PEAK 51(XP21.1) MUTATED	43	8	23
DEL PEAK 51(XP21.1) WILD-TYPE	120	124	80

Figure S1081. Get High-res Image Gene #101: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/22534122/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/22553827/UCEC-TP.transferedmergedcluster.txt
Number of patients = 539
Number of significantly focal cnvs = 101
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

Made with Nozzle