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 100 focal events and 12 molecular subtypes across 539 patients, 748 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p35.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p34.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q44 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_2q13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3p14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_6p24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_8p11.22 cnv correlated to 'CN_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF'.
amp_11p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_14q32.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', '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', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_1p36.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p21.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_9q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q23 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q21 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.43 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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 100 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, 748 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 3q26 2	175 (32%)	364	6e-05 (0.0304)	2e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00015 (0.0723)	0.00816 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 20q11 21	152 (28%)	387	0.0004 (0.183)	3e-05 (0.0162)	1e-05 (0.0118)	1e-05 (0.0118)	0.0004 (0.183)	0.108 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)
del 9q21 2	129 (24%)	410	6e-05 (0.0304)	5e-05 (0.0258)	1e-05 (0.0118)	1e-05 (0.0118)	0.00035 (0.161)	0.696 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00037 (0.17)	1e-05 (0.0118)
del 9q34 2	132 (24%)	407	3e-05 (0.0162)	4e-05 (0.021)	1e-05 (0.0118)	1e-05 (0.0118)	0.00045 (0.203)	0.34 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	7e-05 (0.0351)	1e-05 (0.0118)
del 19p13 3	154 (29%)	385	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	0.0114 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 3q26 2	164 (30%)	375	0.00038 (0.174)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00061 (0.263)	0.016 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 17q25 1	105 (19%)	434	2e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00495 (1.00)	0.109 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	5e-05 (0.0258)
amp 19p13 2	99 (18%)	440	0.00387 (1.00)	0.0001 (0.0494)	1e-05 (0.0118)	1e-05 (0.0118)	0.0193 (1.00)	0.00047 (0.21)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 22q13 32	141 (26%)	398	5e-05 (0.0258)	3e-05 (0.0162)	1e-05 (0.0118)	1e-05 (0.0118)	0.00117 (0.477)	0.131 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	7e-05 (0.0351)	2e-05 (0.0118)
amp 6p24 2	117 (22%)	422	0.00254 (0.97)	0.00069 (0.295)	1e-05 (0.0118)	1e-05 (0.0118)	0.0001 (0.0494)	0.218 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	4e-05 (0.021)
amp 8q24 21	209 (39%)	330	0.0121 (1.00)	0.0714 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	0.0254 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 8q24 21	215 (40%)	324	0.00273 (1.00)	0.00573 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	0.00715 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 19q12	121 (22%)	418	0.00515 (1.00)	3e-05 (0.0162)	1e-05 (0.0118)	1e-05 (0.0118)	0.00463 (1.00)	0.00155 (0.618)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 4q22 1	106 (20%)	433	0.00365 (1.00)	0.0001 (0.0494)	1e-05 (0.0118)	1e-05 (0.0118)	0.014 (1.00)	0.225 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 4q34 3	130 (24%)	409	0.00407 (1.00)	0.00011 (0.054)	1e-05 (0.0118)	1e-05 (0.0118)	0.0622 (1.00)	0.575 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 5q12 1	111 (21%)	428	0.0125 (1.00)	0.00993 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00021 (0.0991)	0.0139 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)
del 7p22 3	72 (13%)	467	0.00014 (0.0679)	0.00181 (0.713)	1e-05 (0.0118)	1e-05 (0.0118)	0.0075 (1.00)	0.0224 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00022 (0.103)	1e-05 (0.0118)
del 8p23 2	119 (22%)	420	0.00201 (0.78)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0447 (1.00)	0.0167 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 8p21 2	117 (22%)	422	0.00212 (0.818)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0196 (1.00)	0.00177 (0.701)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 15q23	115 (21%)	424	0.0017 (0.675)	0.00053 (0.233)	1e-05 (0.0118)	1e-05 (0.0118)	0.119 (1.00)	0.741 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 16q21	154 (29%)	385	0.00087 (0.365)	8e-05 (0.0398)	1e-05 (0.0118)	1e-05 (0.0118)	0.0895 (1.00)	0.54 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 16q23 1	166 (31%)	373	0.00319 (1.00)	0.00014 (0.0679)	1e-05 (0.0118)	1e-05 (0.0118)	0.0359 (1.00)	0.9 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 17p13 3	122 (23%)	417	0.00078 (0.33)	2e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00166 (0.661)	0.477 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	5e-05 (0.0258)
del 17p11 2	128 (24%)	411	0.00075 (0.318)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00366 (1.00)	0.142 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 17q21 31	114 (21%)	425	2e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00446 (1.00)	0.397 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00011 (0.054)	0.00112 (0.458)
amp 1p35 2	56 (10%)	483	0.0517 (1.00)	0.00047 (0.21)	1e-05 (0.0118)	1e-05 (0.0118)	0.00078 (0.33)	0.14 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0361 (1.00)	0.00019 (0.0899)
amp 2q13	119 (22%)	420	0.158 (1.00)	0.0291 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0022 (0.845)	0.0342 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 5p15 33	89 (17%)	450	0.233 (1.00)	0.044 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.292 (1.00)	0.447 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 6p22 3	107 (20%)	432	0.188 (1.00)	0.115 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0224 (1.00)	0.641 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 9p24 2	65 (12%)	474	0.128 (1.00)	0.0882 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00141 (0.567)	0.0087 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00018 (0.0853)	0.00015 (0.0723)
amp 12p12 1	93 (17%)	446	0.329 (1.00)	0.539 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.523 (1.00)	0.988 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00044 (0.2)	5e-05 (0.0258)
amp 12q13 2	100 (19%)	439	0.181 (1.00)	0.0871 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.333 (1.00)	0.614 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00025 (0.116)
amp 13q34	58 (11%)	481	0.692 (1.00)	0.168 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.223 (1.00)	0.0284 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00047 (0.21)	1e-05 (0.0118)
amp 17q11 2	71 (13%)	468	0.151 (1.00)	0.0498 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00757 (1.00)	0.0688 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 17q12	75 (14%)	464	0.105 (1.00)	0.0021 (0.813)	1e-05 (0.0118)	1e-05 (0.0118)	0.006 (1.00)	0.0537 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	4e-05 (0.021)	1e-05 (0.0118)
amp 18p11 31	96 (18%)	443	0.155 (1.00)	0.0542 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00502 (1.00)	0.0884 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 18q11 2	69 (13%)	470	0.108 (1.00)	0.182 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.18 (1.00)	0.0227 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 20p13	117 (22%)	422	0.151 (1.00)	0.0498 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.122 (1.00)	0.269 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0005 (0.221)	1e-05 (0.0118)
amp 20q13 12	152 (28%)	387	0.0129 (1.00)	0.0101 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00562 (1.00)	0.331 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 20q13 33	153 (28%)	386	0.009 (1.00)	0.00139 (0.56)	1e-05 (0.0118)	1e-05 (0.0118)	0.0451 (1.00)	0.61 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
amp 22q12 2	62 (12%)	477	0.379 (1.00)	0.195 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.113 (1.00)	0.00456 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 3p14 2	79 (15%)	460	0.0518 (1.00)	0.00752 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0031 (1.00)	0.0733 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00027 (0.125)	1e-05 (0.0118)
del 4p16 3	94 (17%)	445	0.0135 (1.00)	0.00104 (0.428)	1e-05 (0.0118)	1e-05 (0.0118)	0.00414 (1.00)	0.409 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	2e-05 (0.0118)
del 4p15 2	98 (18%)	441	0.0128 (1.00)	0.0101 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00805 (1.00)	0.498 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)
del 7q31 1	55 (10%)	484	0.137 (1.00)	0.165 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0608 (1.00)	0.0125 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00032 (0.148)	0.00053 (0.233)
del 7q36 1	63 (12%)	476	0.334 (1.00)	0.079 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0106 (1.00)	0.00371 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00012 (0.0587)	3e-05 (0.0162)
del 11p15 5	106 (20%)	433	0.381 (1.00)	0.194 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.288 (1.00)	0.0672 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 11q14 1	70 (13%)	469			1e-05 (0.0118)	1e-05 (0.0118)	0.505 (1.00)	0.585 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 11q25	93 (17%)	446			1e-05 (0.0118)	1e-05 (0.0118)	0.111 (1.00)	1 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 12q23 1	56 (10%)	483			1e-05 (0.0118)	1e-05 (0.0118)	0.038 (1.00)	0.0223 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	5e-05 (0.0258)	1e-05 (0.0118)
del 12q24 33	66 (12%)	473			1e-05 (0.0118)	1e-05 (0.0118)	0.0427 (1.00)	0.038 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	1e-05 (0.0118)
del 15q15 1	140 (26%)	399	0.0507 (1.00)	0.0103 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.00259 (0.987)	0.292 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 16p13 3	92 (17%)	447	0.0129 (1.00)	0.0099 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0633 (1.00)	0.0472 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)
del 16q22 3	158 (29%)	381	0.0332 (1.00)	0.0105 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0778 (1.00)	0.867 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)
del 18q23	98 (18%)	441	0.62 (1.00)	0.252 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0408 (1.00)	0.871 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00026 (0.121)	0.00013 (0.0632)
del 19q13 43	67 (12%)	472	0.00059 (0.256)	4e-05 (0.021)	1e-05 (0.0118)	1e-05 (0.0118)	0.107 (1.00)	0.19 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00994 (1.00)	1e-05 (0.0118)
del xp21 1	88 (16%)	451	0.00074 (0.314)	0.00108 (0.443)	1e-05 (0.0118)	1e-05 (0.0118)	0.00269 (1.00)	0.821 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00015 (0.0723)	1e-05 (0.0118)
amp 1p34 2	73 (14%)	466	0.0132 (1.00)	0.001 (0.415)	1e-05 (0.0118)	1e-05 (0.0118)	0.0201 (1.00)	0.107 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00179 (0.707)	1e-05 (0.0118)
amp 1p22 3	96 (18%)	443	0.0195 (1.00)	0.0152 (1.00)	1e-05 (0.0118)	0.00059 (0.256)	0.896 (1.00)	0.847 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)	0.00024 (0.112)	1e-05 (0.0118)
amp 1q21 3	242 (45%)	297	0.0147 (1.00)	0.00561 (1.00)	1e-05 (0.0118)	0.00036 (0.166)	0.413 (1.00)	0.298 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)	0.00435 (1.00)	1e-05 (0.0118)
amp 1q22	256 (47%)	283	0.022 (1.00)	0.0108 (1.00)	1e-05 (0.0118)	5e-05 (0.0258)	0.199 (1.00)	0.199 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	2e-05 (0.0118)	1e-05 (0.0118)	0.0531 (1.00)	0.00017 (0.0811)
amp 2p24 3	121 (22%)	418	0.683 (1.00)	0.132 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0477 (1.00)	0.246 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00015 (0.0723)	0.00079 (0.333)
amp 3p25 1	82 (15%)	457	0.189 (1.00)	0.0521 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0327 (1.00)	0.299 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	0.00147 (0.589)
amp 4p16 3	53 (10%)	486	0.0502 (1.00)	0.00783 (1.00)	1e-05 (0.0118)	4e-05 (0.021)	0.0912 (1.00)	0.00096 (0.4)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00131 (0.532)	0.00046 (0.207)
amp 5q35 3	57 (11%)	482	0.136 (1.00)	0.166 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.124 (1.00)	0.933 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00057 (0.248)	0.00126 (0.513)
amp 6q25 1	88 (16%)	451	0.284 (1.00)	1 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.088 (1.00)	0.459 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	1e-05 (0.0118)	3e-05 (0.0162)	0.0308 (1.00)
amp 12q13 11	87 (16%)	452	0.378 (1.00)	0.202 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.566 (1.00)	0.662 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00137 (0.553)	0.00044 (0.2)
amp 16p11 2	66 (12%)	473	0.00835 (1.00)	0.00476 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0644 (1.00)	0.099 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00306 (1.00)	0.00046 (0.207)
del 1p36 21	71 (13%)	468	0.0242 (1.00)	0.00185 (0.727)	1e-05 (0.0118)	1e-05 (0.0118)	0.00482 (1.00)	0.271 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00147 (0.589)	0.00021 (0.0991)
del 1p36 11	83 (15%)	456	0.052 (1.00)	0.00756 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0236 (1.00)	0.618 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00101 (0.417)	1e-05 (0.0118)
del 6q26	46 (9%)	493	0.381 (1.00)	0.0296 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.714 (1.00)	0.131 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00062 (0.266)	8e-05 (0.0398)
del 10q23 31	77 (14%)	462	0.135 (1.00)	0.168 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0708 (1.00)	1 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00071 (0.302)	1e-05 (0.0118)
del 14q13 1	73 (14%)	466	0.00841 (1.00)	0.00493 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0601 (1.00)	0.181 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.001 (0.415)	1e-05 (0.0118)
del 17q11 2	105 (19%)	434	0.00059 (0.256)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0198 (1.00)	0.819 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00369 (1.00)	0.00291 (1.00)
del 18q21 2	91 (17%)	448	0.617 (1.00)	0.253 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.043 (1.00)	0.726 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00191 (0.749)	4e-05 (0.021)
del 19p12	58 (11%)	481			1e-05 (0.0118)	1e-05 (0.0118)	0.357 (1.00)	0.456 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0325 (1.00)	5e-05 (0.0258)
amp 3p14 1	65 (12%)	474	0.538 (1.00)	0.516 (1.00)	1e-05 (0.0118)	0.00023 (0.108)	0.0328 (1.00)	0.664 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	5e-05 (0.0258)	1e-05 (0.0118)	0.00335 (1.00)	0.173 (1.00)
amp 8p11 21	162 (30%)	377	0.0107 (1.00)	0.03 (1.00)	1e-05 (0.0118)	0.0028 (1.00)	0.00104 (0.428)	0.052 (1.00)	1e-05 (0.0118)	2e-05 (0.0118)	0.00012 (0.0587)	1e-05 (0.0118)	6e-05 (0.0304)	0.00199 (0.776)
amp 9q34 3	39 (7%)	500	0.242 (1.00)	0.0139 (1.00)	1e-05 (0.0118)	6e-05 (0.0304)	0.326 (1.00)	0.696 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	5e-05 (0.0258)	1e-05 (0.0118)	0.0431 (1.00)	0.0029 (1.00)
amp 11p11 2	51 (9%)	488	0.00213 (0.82)	0.00722 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0289 (1.00)	0.078 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.024 (1.00)	0.0417 (1.00)
amp 11q13 2	74 (14%)	465	0.00196 (0.766)	0.00753 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0824 (1.00)	0.189 (1.00)	1e-05 (0.0118)	2e-05 (0.0118)	4e-05 (0.021)	1e-05 (0.0118)	0.06 (1.00)	0.00895 (1.00)
amp 11q14 1	59 (11%)	480	0.379 (1.00)	0.197 (1.00)	1e-05 (0.0118)	2e-05 (0.0118)	0.454 (1.00)	0.186 (1.00)	2e-05 (0.0118)	1e-05 (0.0118)	3e-05 (0.0162)	2e-05 (0.0118)	0.0167 (1.00)	0.0249 (1.00)
amp 14q24 3	64 (12%)	475	0.06 (1.00)	0.0107 (1.00)	1e-05 (0.0118)	2e-05 (0.0118)	0.0536 (1.00)	0.269 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0653 (1.00)	0.0451 (1.00)
amp 14q32 33	79 (15%)	460	0.432 (1.00)	0.315 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0778 (1.00)	0.632 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00281 (1.00)	0.0257 (1.00)
del 2q22 1	48 (9%)	491	0.0391 (1.00)	0.00067 (0.287)	1e-05 (0.0118)	1e-05 (0.0118)	0.0571 (1.00)	0.0109 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	9e-05 (0.0445)	0.00095 (0.397)	0.00098 (0.408)
del 3q13 31	43 (8%)	496	0.616 (1.00)	0.184 (1.00)	1e-05 (0.0118)	0.00046 (0.207)	0.156 (1.00)	0.14 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00047 (0.21)	0.0159 (1.00)	0.312 (1.00)
del 7q11 22	41 (8%)	498			1e-05 (0.0118)	1e-05 (0.0118)	0.038 (1.00)	0.0152 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.00739 (1.00)	0.00136 (0.551)
del 9p23	79 (15%)	460	0.381 (1.00)	0.029 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0162 (1.00)	0.393 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.022 (1.00)	0.0066 (1.00)
del 13q11	98 (18%)	441	0.332 (1.00)	0.0398 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.188 (1.00)	0.813 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0257 (1.00)	0.0066 (1.00)
del 13q14 2	107 (20%)	432	0.619 (1.00)	0.0655 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	0.0776 (1.00)	0.696 (1.00)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	1e-05 (0.0118)	0.0212 (1.00)	0.00289 (1.00)
amp 7q31 2	93 (17%)	446	0.535 (1.00)	0.435 (1.00)	1e-05 (0.0118)	0.00014 (0.0679)	0.648 (1.00)	0.496 (1.00)	0.00024 (0.112)	0.00017 (0.0811)	0.00047 (0.21)	0.0113 (1.00)	0.0217 (1.00)	0.0146 (1.00)
amp 15q26 3	38 (7%)	501			1e-05 (0.0118)	0.00901 (1.00)	0.0727 (1.00)	0.716 (1.00)	1e-05 (0.0118)	2e-05 (0.0118)	4e-05 (0.021)	7e-05 (0.0351)	0.123 (1.00)	0.162 (1.00)
amp xp11 23	90 (17%)	449	0.356 (1.00)	0.815 (1.00)	1e-05 (0.0118)	0.00022 (0.103)	0.726 (1.00)	0.863 (1.00)	0.00015 (0.0723)	2e-05 (0.0118)	0.00061 (0.263)	0.00051 (0.225)	0.00886 (1.00)	0.0101 (1.00)
del 2p25 3	26 (5%)	513			1e-05 (0.0118)	0.00017 (0.0811)	0.27 (1.00)	0.0928 (1.00)	7e-05 (0.0351)	8e-05 (0.0398)	0.00041 (0.187)	0.00412 (1.00)	0.175 (1.00)	0.141 (1.00)
del 2q37 3	53 (10%)	486			1e-05 (0.0118)	2e-05 (0.0118)	0.244 (1.00)	0.815 (1.00)	1e-05 (0.0118)	3e-05 (0.0162)	1e-05 (0.0118)	0.0101 (1.00)	0.199 (1.00)	0.124 (1.00)
del 20p12 1	36 (7%)	503	1 (1.00)	0.516 (1.00)	1e-05 (0.0118)	0.0435 (1.00)	0.141 (1.00)	0.557 (1.00)	0.00053 (0.233)	0.00044 (0.2)	0.00056 (0.244)	0.00051 (0.225)	0.0893 (1.00)	0.19 (1.00)
amp 1q44	218 (40%)	321	0.0314 (1.00)	0.0385 (1.00)	1e-05 (0.0118)	0.0368 (1.00)	0.732 (1.00)	0.107 (1.00)	0.00345 (1.00)	0.00199 (0.776)	3e-05 (0.0162)	0.00431 (1.00)	0.866 (1.00)	0.0648 (1.00)
amp xq28	93 (17%)	446	0.0855 (1.00)	0.0255 (1.00)	1e-05 (0.0118)	0.0313 (1.00)	0.225 (1.00)	0.727 (1.00)	0.00089 (0.373)	0.00012 (0.0587)	0.00262 (0.996)	0.00246 (0.942)	0.0179 (1.00)	0.167 (1.00)
amp 8p11 22	126 (23%)	413	0.087 (1.00)	0.228 (1.00)	1e-05 (0.0118)	1 (1.00)	0.0354 (1.00)	0.424 (1.00)	0.176 (1.00)	0.941 (1.00)	0.52 (1.00)	0.0698 (1.00)	0.721 (1.00)	0.75 (1.00)
amp 10q22 2	143 (27%)	396	0.0314 (1.00)	0.114 (1.00)	1e-05 (0.0118)	0.184 (1.00)	0.31 (1.00)	0.552 (1.00)	0.0119 (1.00)	0.00266 (1.00)	0.491 (1.00)	0.00365 (1.00)	0.976 (1.00)	0.19 (1.00)

'amp_1p35.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.21

Table S1. 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 S1. 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 = 0.012

Table S2. Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 1(1P35.2) MUTATED	54	0	1	0	1
AMP PEAK 1(1P35.2) WILD-TYPE	115	305	18	9	36

Figure S2. 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 = 0.012

Table S3. Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 1(1P35.2) MUTATED	35	4	6
AMP PEAK 1(1P35.2) WILD-TYPE	130	85	165

Figure S3. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S4. Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 1(1P35.2) MUTATED	0	48	6
AMP PEAK 1(1P35.2) WILD-TYPE	151	182	143

Figure S4. 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 = 0.012

Table S5. Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 1(1P35.2) MUTATED	6	42	6
AMP PEAK 1(1P35.2) WILD-TYPE	210	127	139

Figure S5. 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 = 0.012

Table S6. Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 1(1P35.2) MUTATED	42	6	5
AMP PEAK 1(1P35.2) WILD-TYPE	184	137	156

Figure S6. 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 = 0.012

Table S7. Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 1(1P35.2) MUTATED	6	1	33	13
AMP PEAK 1(1P35.2) WILD-TYPE	135	59	90	193

Figure S7. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.09

Table S8. Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 1(1P35.2) MUTATED	28	6	8
AMP PEAK 1(1P35.2) WILD-TYPE	116	109	131

Figure S8. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S9. Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 2(1P34.2) MUTATED	71	0	1	0	1
AMP PEAK 2(1P34.2) WILD-TYPE	98	305	18	9	36

Figure S9. 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 = 0.012

Table S10. Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 2(1P34.2) MUTATED	48	10	5
AMP PEAK 2(1P34.2) WILD-TYPE	117	79	166

Figure S10. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S11. Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 2(1P34.2) MUTATED	1	63	6
AMP PEAK 2(1P34.2) WILD-TYPE	150	167	143

Figure S11. 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 = 0.012

Table S12. Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 2(1P34.2) MUTATED	7	57	6
AMP PEAK 2(1P34.2) WILD-TYPE	209	112	139

Figure S12. 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 = 0.012

Table S13. Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 2(1P34.2) MUTATED	62	5	4
AMP PEAK 2(1P34.2) WILD-TYPE	164	138	157

Figure S13. 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 = 0.012

Table S14. Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 2(1P34.2) MUTATED	5	1	47	18
AMP PEAK 2(1P34.2) WILD-TYPE	136	59	76	188

Figure S14. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S15. Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 2(1P34.2) MUTATED	39	5	15
AMP PEAK 2(1P34.2) WILD-TYPE	105	110	124

Figure S15. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S16. Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 3(1P22.3) MUTATED	53	30	2	7	4
AMP PEAK 3(1P22.3) WILD-TYPE	116	275	17	2	33

Figure S16. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S17. Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 3(1P22.3) MUTATED	26	59	8
AMP PEAK 3(1P22.3) WILD-TYPE	125	171	141

Figure S17. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S18. Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 3(1P22.3) MUTATED	37	49	7
AMP PEAK 3(1P22.3) WILD-TYPE	179	120	138

Figure S18. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S19. Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 3(1P22.3) MUTATED	54	33	8
AMP PEAK 3(1P22.3) WILD-TYPE	172	110	153

Figure S19. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S20. Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 3(1P22.3) MUTATED	11	9	39	36
AMP PEAK 3(1P22.3) WILD-TYPE	130	51	84	170

Figure S20. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.11

Table S21. Gene #3: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 3(1P22.3) MUTATED	48	13	14
AMP PEAK 3(1P22.3) WILD-TYPE	124	83	116

Figure S21. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S22. Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 3(1P22.3) MUTATED	46	8	21
AMP PEAK 3(1P22.3) WILD-TYPE	98	107	118

Figure S22. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S23. Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 4(1Q21.3) MUTATED	105	90	13	9	25
AMP PEAK 4(1Q21.3) WILD-TYPE	64	215	6	0	12

Figure S23. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.17

Table S24. Gene #4: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 4(1Q21.3) MUTATED	92	31	62
AMP PEAK 4(1Q21.3) WILD-TYPE	73	58	109

Figure S24. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S25. Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 4(1Q21.3) MUTATED	69	128	41
AMP PEAK 4(1Q21.3) WILD-TYPE	82	102	108

Figure S25. Get High-res Image Gene #4: '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 = 0.012

Table S26. Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 4(1Q21.3) MUTATED	96	103	39
AMP PEAK 4(1Q21.3) WILD-TYPE	120	66	106

Figure S26. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S27. Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 4(1Q21.3) MUTATED	119	75	45
AMP PEAK 4(1Q21.3) WILD-TYPE	107	68	116

Figure S27. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S28. Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 4(1Q21.3) MUTATED	44	30	80	85
AMP PEAK 4(1Q21.3) WILD-TYPE	97	30	43	121

Figure S28. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S29. Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 4(1Q21.3) MUTATED	88	37	56
AMP PEAK 4(1Q21.3) WILD-TYPE	56	78	83

Figure S29. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S30. Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 5(1Q22) MUTATED	116	93	13	9	25
AMP PEAK 5(1Q22) WILD-TYPE	53	212	6	0	12

Figure S30. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S31. Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 5(1Q22) MUTATED	100	34	63
AMP PEAK 5(1Q22) WILD-TYPE	65	55	108

Figure S31. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S32. Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 5(1Q22) MUTATED	70	137	45
AMP PEAK 5(1Q22) WILD-TYPE	81	93	104

Figure S32. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S33. Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 5(1Q22) MUTATED	98	111	43
AMP PEAK 5(1Q22) WILD-TYPE	118	58	102

Figure S33. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S34. Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 5(1Q22) MUTATED	126	77	50
AMP PEAK 5(1Q22) WILD-TYPE	100	66	111

Figure S34. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S35. Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 5(1Q22) MUTATED	48	31	88	86
AMP PEAK 5(1Q22) WILD-TYPE	93	29	35	120

Figure S35. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.081

Table S36. Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 5(1Q22) MUTATED	89	42	62
AMP PEAK 5(1Q22) WILD-TYPE	55	73	77

Figure S36. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S37. Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 6(1Q44) MUTATED	83	92	10	9	24
AMP PEAK 6(1Q44) WILD-TYPE	86	213	9	0	13

Figure S37. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S38. Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 6(1Q44) MUTATED	91	79	46
AMP PEAK 6(1Q44) WILD-TYPE	135	64	115

Figure S38. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S39. Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 7(2P24.3) MUTATED	79	14	12	4	12
AMP PEAK 7(2P24.3) WILD-TYPE	90	291	7	5	25

Figure S39. Get High-res Image Gene #7: '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 = 0.012

Table S40. Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 7(2P24.3) MUTATED	66	11	19
AMP PEAK 7(2P24.3) WILD-TYPE	99	78	152

Figure S40. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S41. Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 7(2P24.3) MUTATED	20	83	16
AMP PEAK 7(2P24.3) WILD-TYPE	131	147	133

Figure S41. Get High-res Image Gene #7: '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 = 0.012

Table S42. Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 7(2P24.3) MUTATED	30	72	17
AMP PEAK 7(2P24.3) WILD-TYPE	186	97	128

Figure S42. Get High-res Image Gene #7: '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 = 0.012

Table S43. Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 7(2P24.3) MUTATED	80	20	19
AMP PEAK 7(2P24.3) WILD-TYPE	146	123	142

Figure S43. Get High-res Image Gene #7: '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 = 0.012

Table S44. Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 7(2P24.3) MUTATED	18	9	59	33
AMP PEAK 7(2P24.3) WILD-TYPE	123	51	64	173

Figure S44. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S45. Gene #7: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 7(2P24.3) MUTATED	56	20	16
AMP PEAK 7(2P24.3) WILD-TYPE	116	76	114

Figure S45. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S46. Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 8(2Q13) MUTATED	90	8	9	3	9
AMP PEAK 8(2Q13) WILD-TYPE	79	297	10	6	28

Figure S46. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S47. Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 8(2Q13) MUTATED	72	14	10
AMP PEAK 8(2Q13) WILD-TYPE	93	75	161

Figure S47. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S48. Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 8(2Q13) MUTATED	12	96	8
AMP PEAK 8(2Q13) WILD-TYPE	139	134	141

Figure S48. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S49. Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 8(2Q13) MUTATED	21	86	9
AMP PEAK 8(2Q13) WILD-TYPE	195	83	136

Figure S49. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S50. Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 8(2Q13) MUTATED	92	16	9
AMP PEAK 8(2Q13) WILD-TYPE	134	127	152

Figure S50. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S51. Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 8(2Q13) MUTATED	12	5	70	30
AMP PEAK 8(2Q13) WILD-TYPE	129	55	53	176

Figure S51. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S52. Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 8(2Q13) MUTATED	61	22	11
AMP PEAK 8(2Q13) WILD-TYPE	111	74	119

Figure S52. Get High-res Image Gene #8: '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 = 0.012

Table S53. Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 8(2Q13) MUTATED	51	8	35
AMP PEAK 8(2Q13) WILD-TYPE	93	107	104

Figure S53. Get High-res Image Gene #8: '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 = 0.012

Table S54. Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 9(3P25.1) MUTATED	62	4	1	3	12
AMP PEAK 9(3P25.1) WILD-TYPE	107	301	18	6	25

Figure S54. Get High-res Image Gene #9: '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 = 0.012

Table S55. Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 9(3P25.1) MUTATED	44	14	10
AMP PEAK 9(3P25.1) WILD-TYPE	121	75	161

Figure S55. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S56. Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 9(3P25.1) MUTATED	4	66	11
AMP PEAK 9(3P25.1) WILD-TYPE	147	164	138

Figure S56. Get High-res Image Gene #9: '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 = 0.012

Table S57. Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 9(3P25.1) MUTATED	16	55	10
AMP PEAK 9(3P25.1) WILD-TYPE	200	114	135

Figure S57. Get High-res Image Gene #9: '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 = 0.012

Table S58. Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 9(3P25.1) MUTATED	58	11	11
AMP PEAK 9(3P25.1) WILD-TYPE	168	132	150

Figure S58. Get High-res Image Gene #9: '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 = 0.012

Table S59. Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 9(3P25.1) MUTATED	13	0	44	23
AMP PEAK 9(3P25.1) WILD-TYPE	128	60	79	183

Figure S59. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S60. Gene #9: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 9(3P25.1) MUTATED	40	18	7
AMP PEAK 9(3P25.1) WILD-TYPE	132	78	123

Figure S60. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S61. Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 10(3P14.1) MUTATED	46	3	1	3	12
AMP PEAK 10(3P14.1) WILD-TYPE	123	302	18	6	25

Figure S61. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p14.1' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.11

Table S62. Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 10(3P14.1) MUTATED	35	10	11
AMP PEAK 10(3P14.1) WILD-TYPE	130	79	160

Figure S62. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S63. Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 10(3P14.1) MUTATED	4	49	11
AMP PEAK 10(3P14.1) WILD-TYPE	147	181	138

Figure S63. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S64. Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 10(3P14.1) MUTATED	15	39	10
AMP PEAK 10(3P14.1) WILD-TYPE	201	130	135

Figure S64. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S65. Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 10(3P14.1) MUTATED	44	10	10
AMP PEAK 10(3P14.1) WILD-TYPE	182	133	151

Figure S65. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S66. Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 10(3P14.1) MUTATED	13	0	31	20
AMP PEAK 10(3P14.1) WILD-TYPE	128	60	92	186

Figure S66. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S67. Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 11(3Q26.2) MUTATED	1	11	1	0
AMP PEAK 11(3Q26.2) WILD-TYPE	13	6	11	10

Figure S67. 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 = 0.012

Table S68. 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	4	8	1	0	0
AMP PEAK 11(3Q26.2) WILD-TYPE	10	1	6	7	16

Figure S68. 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 = 0.012

Table S69. Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 11(3Q26.2) MUTATED	141	11	3	5	15
AMP PEAK 11(3Q26.2) WILD-TYPE	28	294	16	4	22

Figure S69. 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 = 0.012

Table S70. Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 11(3Q26.2) MUTATED	102	25	23
AMP PEAK 11(3Q26.2) WILD-TYPE	63	64	148

Figure S70. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S71. Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
AMP PEAK 11(3Q26.2) MUTATED	11	15	4	1	1	6
AMP PEAK 11(3Q26.2) WILD-TYPE	30	22	35	11	40	18

Figure S71. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S72. Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 11(3Q26.2) MUTATED	8	140	23
AMP PEAK 11(3Q26.2) WILD-TYPE	143	90	126

Figure S72. 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 = 0.012

Table S73. Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 11(3Q26.2) MUTATED	28	120	23
AMP PEAK 11(3Q26.2) WILD-TYPE	188	49	122

Figure S73. 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 = 0.012

Table S74. Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 11(3Q26.2) MUTATED	133	16	22
AMP PEAK 11(3Q26.2) WILD-TYPE	93	127	139

Figure S74. 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 = 0.012

Table S75. Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 11(3Q26.2) MUTATED	26	0	91	54
AMP PEAK 11(3Q26.2) WILD-TYPE	115	60	32	152

Figure S75. 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 = 0.012

Table S76. Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 11(3Q26.2) MUTATED	85	33	25
AMP PEAK 11(3Q26.2) WILD-TYPE	87	63	105

Figure S76. 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 = 0.012

Table S77. Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 11(3Q26.2) MUTATED	78	20	45
AMP PEAK 11(3Q26.2) WILD-TYPE	66	95	94

Figure S77. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.17

Table S78. Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 12(3Q26.2) MUTATED	1	10	1	0
AMP PEAK 12(3Q26.2) WILD-TYPE	13	7	11	10

Figure S78. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S79. Gene #12: '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 12(3Q26.2) MUTATED	3	8	1	0	0
AMP PEAK 12(3Q26.2) WILD-TYPE	11	1	6	7	16

Figure S79. Get High-res Image Gene #12: '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 = 0.012

Table S80. Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 12(3Q26.2) MUTATED	135	7	3	5	14
AMP PEAK 12(3Q26.2) WILD-TYPE	34	298	16	4	23

Figure S80. Get High-res Image Gene #12: '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 = 0.012

Table S81. Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 12(3Q26.2) MUTATED	101	20	20
AMP PEAK 12(3Q26.2) WILD-TYPE	64	69	151

Figure S81. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S82. Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 12(3Q26.2) MUTATED	8	133	19
AMP PEAK 12(3Q26.2) WILD-TYPE	143	97	130

Figure S82. Get High-res Image Gene #12: '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 = 0.012

Table S83. Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 12(3Q26.2) MUTATED	26	115	19
AMP PEAK 12(3Q26.2) WILD-TYPE	190	54	126

Figure S83. Get High-res Image Gene #12: '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 = 0.012

Table S84. Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 12(3Q26.2) MUTATED	125	17	18
AMP PEAK 12(3Q26.2) WILD-TYPE	101	126	143

Figure S84. Get High-res Image Gene #12: '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 = 0.012

Table S85. Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 12(3Q26.2) MUTATED	22	0	88	50
AMP PEAK 12(3Q26.2) WILD-TYPE	119	60	35	156

Figure S85. Get High-res Image Gene #12: '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 = 0.012

Table S86. Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 12(3Q26.2) MUTATED	84	28	22
AMP PEAK 12(3Q26.2) WILD-TYPE	88	68	108

Figure S86. Get High-res Image Gene #12: '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 = 0.012

Table S87. Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 12(3Q26.2) MUTATED	77	16	41
AMP PEAK 12(3Q26.2) WILD-TYPE	67	99	98

Figure S87. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S88. Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 13(4P16.3) MUTATED	50	2	0	0	1
AMP PEAK 13(4P16.3) WILD-TYPE	119	303	19	9	36

Figure S88. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S89. Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 13(4P16.3) MUTATED	30	8	6
AMP PEAK 13(4P16.3) WILD-TYPE	135	81	165

Figure S89. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S90. Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 13(4P16.3) MUTATED	1	49	2
AMP PEAK 13(4P16.3) WILD-TYPE	150	181	147

Figure S90. Get High-res Image Gene #13: '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 = 0.012

Table S91. Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 13(4P16.3) MUTATED	7	42	3
AMP PEAK 13(4P16.3) WILD-TYPE	209	127	142

Figure S91. Get High-res Image Gene #13: '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 = 0.012

Table S92. Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 13(4P16.3) MUTATED	44	3	4
AMP PEAK 13(4P16.3) WILD-TYPE	182	140	157

Figure S92. Get High-res Image Gene #13: '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 = 0.012

Table S93. Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 13(4P16.3) MUTATED	5	0	33	13
AMP PEAK 13(4P16.3) WILD-TYPE	136	60	90	193

Figure S93. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.21

Table S94. Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 13(4P16.3) MUTATED	26	4	12
AMP PEAK 13(4P16.3) WILD-TYPE	118	111	127

Figure S94. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S95. Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 14(5P15.33) MUTATED	80	4	4	1	0
AMP PEAK 14(5P15.33) WILD-TYPE	89	301	15	8	37

Figure S95. Get High-res Image Gene #14: '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 = 0.012

Table S96. Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 14(5P15.33) MUTATED	58	11	7
AMP PEAK 14(5P15.33) WILD-TYPE	107	78	164

Figure S96. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S97. Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 14(5P15.33) MUTATED	5	78	4
AMP PEAK 14(5P15.33) WILD-TYPE	146	152	145

Figure S97. Get High-res Image Gene #14: '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 = 0.012

Table S98. Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 14(5P15.33) MUTATED	16	66	5
AMP PEAK 14(5P15.33) WILD-TYPE	200	103	140

Figure S98. Get High-res Image Gene #14: '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 = 0.012

Table S99. Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 14(5P15.33) MUTATED	72	11	5
AMP PEAK 14(5P15.33) WILD-TYPE	154	132	156

Figure S99. Get High-res Image Gene #14: '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 = 0.012

Table S100. Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 14(5P15.33) MUTATED	6	4	53	25
AMP PEAK 14(5P15.33) WILD-TYPE	135	56	70	181

Figure S100. Get High-res Image Gene #14: '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 = 0.012

Table S101. Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 14(5P15.33) MUTATED	54	15	6
AMP PEAK 14(5P15.33) WILD-TYPE	118	81	124

Figure S101. Get High-res Image Gene #14: '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 = 0.012

Table S102. Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 14(5P15.33) MUTATED	47	4	24
AMP PEAK 14(5P15.33) WILD-TYPE	97	111	115

Figure S102. Get High-res Image Gene #14: '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 = 0.012

Table S103. Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 15(5Q35.3) MUTATED	51	1	4	1	0
AMP PEAK 15(5Q35.3) WILD-TYPE	118	304	15	8	37

Figure S103. Get High-res Image Gene #15: '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 = 0.012

Table S104. Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 15(5Q35.3) MUTATED	35	9	6
AMP PEAK 15(5Q35.3) WILD-TYPE	130	80	165

Figure S104. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S105. Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 15(5Q35.3) MUTATED	4	49	3
AMP PEAK 15(5Q35.3) WILD-TYPE	147	181	146

Figure S105. Get High-res Image Gene #15: '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 = 0.012

Table S106. Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 15(5Q35.3) MUTATED	11	42	3
AMP PEAK 15(5Q35.3) WILD-TYPE	205	127	142

Figure S106. Get High-res Image Gene #15: '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 = 0.012

Table S107. Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 15(5Q35.3) MUTATED	45	7	4
AMP PEAK 15(5Q35.3) WILD-TYPE	181	136	157

Figure S107. Get High-res Image Gene #15: '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 = 0.012

Table S108. Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 15(5Q35.3) MUTATED	5	4	32	15
AMP PEAK 15(5Q35.3) WILD-TYPE	136	56	91	191

Figure S108. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.25

Table S109. Gene #15: 'amp_5q35.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 15(5Q35.3) MUTATED	30	13	5
AMP PEAK 15(5Q35.3) WILD-TYPE	142	83	125

Figure S109. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S110. Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 16(6P24.2) MUTATED	95	8	1	1	12
AMP PEAK 16(6P24.2) WILD-TYPE	74	297	18	8	25

Figure S110. Get High-res Image Gene #16: '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 = 0.012

Table S111. Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 16(6P24.2) MUTATED	73	15	12
AMP PEAK 16(6P24.2) WILD-TYPE	92	74	159

Figure S111. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p24.2' versus 'RPPA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.049

Table S112. Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
AMP PEAK 16(6P24.2) MUTATED	5	13	2	1	0	3
AMP PEAK 16(6P24.2) WILD-TYPE	36	24	37	11	41	21

Figure S112. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S113. Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 16(6P24.2) MUTATED	6	96	15
AMP PEAK 16(6P24.2) WILD-TYPE	145	134	134

Figure S113. Get High-res Image Gene #16: '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 = 0.012

Table S114. Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 16(6P24.2) MUTATED	24	79	14
AMP PEAK 16(6P24.2) WILD-TYPE	192	90	131

Figure S114. Get High-res Image Gene #16: '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 = 0.012

Table S115. Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 16(6P24.2) MUTATED	86	16	12
AMP PEAK 16(6P24.2) WILD-TYPE	140	127	149

Figure S115. Get High-res Image Gene #16: '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 = 0.012

Table S116. Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 16(6P24.2) MUTATED	12	1	63	38
AMP PEAK 16(6P24.2) WILD-TYPE	129	59	60	168

Figure S116. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S117. Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 16(6P24.2) MUTATED	58	24	14
AMP PEAK 16(6P24.2) WILD-TYPE	114	72	116

Figure S117. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S118. Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 16(6P24.2) MUTATED	51	13	32
AMP PEAK 16(6P24.2) WILD-TYPE	93	102	107

Figure S118. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S119. Gene #17: 'amp_6p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 17(6P22.3) MUTATED	86	7	1	1	12
AMP PEAK 17(6P22.3) WILD-TYPE	83	298	18	8	25

Figure S119. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S120. Gene #17: 'amp_6p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 17(6P22.3) MUTATED	70	15	10
AMP PEAK 17(6P22.3) WILD-TYPE	95	74	161

Figure S120. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S121. Gene #17: 'amp_6p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 17(6P22.3) MUTATED	6	86	14
AMP PEAK 17(6P22.3) WILD-TYPE	145	144	135

Figure S121. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S122. Gene #17: 'amp_6p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 17(6P22.3) MUTATED	21	72	13
AMP PEAK 17(6P22.3) WILD-TYPE	195	97	132

Figure S122. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S123. Gene #17: 'amp_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 17(6P22.3) MUTATED	81	14	11
AMP PEAK 17(6P22.3) WILD-TYPE	145	129	150

Figure S123. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S124. Gene #17: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 17(6P22.3) MUTATED	11	1	59	35
AMP PEAK 17(6P22.3) WILD-TYPE	130	59	64	171

Figure S124. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S125. Gene #17: 'amp_6p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 17(6P22.3) MUTATED	58	21	12
AMP PEAK 17(6P22.3) WILD-TYPE	114	75	118

Figure S125. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S126. Gene #17: 'amp_6p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 17(6P22.3) MUTATED	50	11	30
AMP PEAK 17(6P22.3) WILD-TYPE	94	104	109

Figure S126. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S127. Gene #18: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 18(6Q25.1) MUTATED	65	7	3	2	11
AMP PEAK 18(6Q25.1) WILD-TYPE	104	298	16	7	26

Figure S127. Get High-res Image Gene #18: '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 = 0.012

Table S128. Gene #18: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 18(6Q25.1) MUTATED	55	10	14
AMP PEAK 18(6Q25.1) WILD-TYPE	110	79	157

Figure S128. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S129. Gene #18: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 18(6Q25.1) MUTATED	8	62	17
AMP PEAK 18(6Q25.1) WILD-TYPE	143	168	132

Figure S129. Get High-res Image Gene #18: '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 = 0.012

Table S130. Gene #18: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 18(6Q25.1) MUTATED	22	48	17
AMP PEAK 18(6Q25.1) WILD-TYPE	194	121	128

Figure S130. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S131. Gene #18: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 18(6Q25.1) MUTATED	57	19	12
AMP PEAK 18(6Q25.1) WILD-TYPE	169	124	149

Figure S131. Get High-res Image Gene #18: '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 = 0.012

Table S132. Gene #18: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 18(6Q25.1) MUTATED	12	2	41	33
AMP PEAK 18(6Q25.1) WILD-TYPE	129	58	82	173

Figure S132. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S133. Gene #18: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 18(6Q25.1) MUTATED	48	17	11
AMP PEAK 18(6Q25.1) WILD-TYPE	124	79	119

Figure S133. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S134. Gene #19: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 19(7Q31.2) MUTATED	53	15	13	2	10
AMP PEAK 19(7Q31.2) WILD-TYPE	116	290	6	7	27

Figure S134. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.068

Table S135. Gene #19: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 19(7Q31.2) MUTATED	45	8	21
AMP PEAK 19(7Q31.2) WILD-TYPE	120	81	150

Figure S135. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.11

Table S136. Gene #19: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 19(7Q31.2) MUTATED	15	56	17
AMP PEAK 19(7Q31.2) WILD-TYPE	136	174	132

Figure S136. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.081

Table S137. Gene #19: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 19(7Q31.2) MUTATED	25	45	18
AMP PEAK 19(7Q31.2) WILD-TYPE	191	124	127

Figure S137. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.21

Table S138. Gene #19: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 19(7Q31.2) MUTATED	56	21	16
AMP PEAK 19(7Q31.2) WILD-TYPE	170	122	145

Figure S138. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S139. Gene #20: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 20(8P11.22) MUTATED	50	29	8	2	37
AMP PEAK 20(8P11.22) WILD-TYPE	119	276	11	7	0

Figure S139. Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S140. Gene #21: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 21(8P11.21) MUTATED	87	29	8	2	36
AMP PEAK 21(8P11.21) WILD-TYPE	82	276	11	7	1

Figure S140. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S141. Gene #21: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 21(8P11.21) MUTATED	30	98	33
AMP PEAK 21(8P11.21) WILD-TYPE	121	132	116

Figure S141. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S142. Gene #21: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 21(8P11.21) MUTATED	50	77	34
AMP PEAK 21(8P11.21) WILD-TYPE	166	92	111

Figure S142. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.059

Table S143. Gene #21: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 21(8P11.21) MUTATED	91	35	33
AMP PEAK 21(8P11.21) WILD-TYPE	135	108	128

Figure S143. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S144. Gene #21: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 21(8P11.21) MUTATED	32	7	60	60
AMP PEAK 21(8P11.21) WILD-TYPE	109	53	63	146

Figure S144. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S145. Gene #21: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 21(8P11.21) MUTATED	75	30	26
AMP PEAK 21(8P11.21) WILD-TYPE	97	66	104

Figure S145. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S146. Gene #22: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 22(8Q24.21) MUTATED	126	35	8	3	37
AMP PEAK 22(8Q24.21) WILD-TYPE	43	270	11	6	0

Figure S146. Get High-res Image Gene #22: '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 = 0.012

Table S147. Gene #22: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 22(8Q24.21) MUTATED	101	32	48
AMP PEAK 22(8Q24.21) WILD-TYPE	64	57	123

Figure S147. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S148. Gene #22: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
AMP PEAK 22(8Q24.21) MUTATED	12	14	8	2	2	14
AMP PEAK 22(8Q24.21) WILD-TYPE	29	23	31	10	39	10

Figure S148. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S149. Gene #22: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 22(8Q24.21) MUTATED	30	137	39
AMP PEAK 22(8Q24.21) WILD-TYPE	121	93	110

Figure S149. Get High-res Image Gene #22: '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 = 0.012

Table S150. Gene #22: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 22(8Q24.21) MUTATED	55	111	40
AMP PEAK 22(8Q24.21) WILD-TYPE	161	58	105

Figure S150. Get High-res Image Gene #22: '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 = 0.012

Table S151. Gene #22: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 22(8Q24.21) MUTATED	131	37	38
AMP PEAK 22(8Q24.21) WILD-TYPE	95	106	123

Figure S151. Get High-res Image Gene #22: '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 = 0.012

Table S152. Gene #22: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 22(8Q24.21) MUTATED	37	8	85	76
AMP PEAK 22(8Q24.21) WILD-TYPE	104	52	38	130

Figure S152. Get High-res Image Gene #22: '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 = 0.012

Table S153. Gene #22: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 22(8Q24.21) MUTATED	95	41	33
AMP PEAK 22(8Q24.21) WILD-TYPE	77	55	97

Figure S153. Get High-res Image Gene #22: '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 = 0.012

Table S154. Gene #22: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 22(8Q24.21) MUTATED	83	30	56
AMP PEAK 22(8Q24.21) WILD-TYPE	61	85	83

Figure S154. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S155. Gene #23: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 23(8Q24.21) MUTATED	127	40	8	3	37
AMP PEAK 23(8Q24.21) WILD-TYPE	42	265	11	6	0

Figure S155. Get High-res Image Gene #23: '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 = 0.012

Table S156. Gene #23: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 23(8Q24.21) MUTATED	101	31	53
AMP PEAK 23(8Q24.21) WILD-TYPE	64	58	118

Figure S156. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S157. Gene #23: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
AMP PEAK 23(8Q24.21) MUTATED	12	17	7	2	2	16
AMP PEAK 23(8Q24.21) WILD-TYPE	29	20	32	10	39	8

Figure S157. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S158. Gene #23: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 23(8Q24.21) MUTATED	33	139	40
AMP PEAK 23(8Q24.21) WILD-TYPE	118	91	109

Figure S158. Get High-res Image Gene #23: '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 = 0.012

Table S159. Gene #23: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 23(8Q24.21) MUTATED	57	114	41
AMP PEAK 23(8Q24.21) WILD-TYPE	159	55	104

Figure S159. Get High-res Image Gene #23: '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 = 0.012

Table S160. Gene #23: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 23(8Q24.21) MUTATED	136	37	38
AMP PEAK 23(8Q24.21) WILD-TYPE	90	106	123

Figure S160. Get High-res Image Gene #23: '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 = 0.012

Table S161. Gene #23: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 23(8Q24.21) MUTATED	40	10	86	75
AMP PEAK 23(8Q24.21) WILD-TYPE	101	50	37	131

Figure S161. Get High-res Image Gene #23: '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 = 0.012

Table S162. Gene #23: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 23(8Q24.21) MUTATED	98	40	36
AMP PEAK 23(8Q24.21) WILD-TYPE	74	56	94

Figure S162. Get High-res Image Gene #23: '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 = 0.012

Table S163. Gene #23: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 23(8Q24.21) MUTATED	88	32	54
AMP PEAK 23(8Q24.21) WILD-TYPE	56	83	85

Figure S163. Get High-res Image Gene #23: '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 = 0.012

Table S164. Gene #24: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 24(9P24.2) MUTATED	59	4	1	0	1
AMP PEAK 24(9P24.2) WILD-TYPE	110	301	18	9	36

Figure S164. Get High-res Image Gene #24: '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 = 0.012

Table S165. Gene #24: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 24(9P24.2) MUTATED	42	7	5
AMP PEAK 24(9P24.2) WILD-TYPE	123	82	166

Figure S165. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S166. Gene #24: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 24(9P24.2) MUTATED	3	57	5
AMP PEAK 24(9P24.2) WILD-TYPE	148	173	144

Figure S166. Get High-res Image Gene #24: '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 = 0.012

Table S167. Gene #24: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 24(9P24.2) MUTATED	15	46	4
AMP PEAK 24(9P24.2) WILD-TYPE	201	123	141

Figure S167. Get High-res Image Gene #24: '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 = 0.012

Table S168. Gene #24: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 24(9P24.2) MUTATED	55	7	2
AMP PEAK 24(9P24.2) WILD-TYPE	171	136	159

Figure S168. Get High-res Image Gene #24: '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 = 0.012

Table S169. Gene #24: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 24(9P24.2) MUTATED	4	2	39	19
AMP PEAK 24(9P24.2) WILD-TYPE	137	58	84	187

Figure S169. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.085

Table S170. Gene #24: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 24(9P24.2) MUTATED	35	11	6
AMP PEAK 24(9P24.2) WILD-TYPE	137	85	124

Figure S170. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S171. Gene #24: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 24(9P24.2) MUTATED	31	5	16
AMP PEAK 24(9P24.2) WILD-TYPE	113	110	123

Figure S171. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S172. Gene #25: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 25(9Q34.3) MUTATED	35	2	0	1	1
AMP PEAK 25(9Q34.3) WILD-TYPE	134	303	19	8	36

Figure S172. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S173. Gene #25: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 25(9Q34.3) MUTATED	22	6	2
AMP PEAK 25(9Q34.3) WILD-TYPE	143	83	169

Figure S173. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S174. Gene #25: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 25(9Q34.3) MUTATED	3	34	1
AMP PEAK 25(9Q34.3) WILD-TYPE	148	196	148

Figure S174. Get High-res Image Gene #25: '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 = 0.012

Table S175. Gene #25: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 25(9Q34.3) MUTATED	4	32	2
AMP PEAK 25(9Q34.3) WILD-TYPE	212	137	143

Figure S175. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S176. Gene #25: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 25(9Q34.3) MUTATED	28	4	3
AMP PEAK 25(9Q34.3) WILD-TYPE	198	139	158

Figure S176. Get High-res Image Gene #25: '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 = 0.012

Table S177. Gene #25: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 25(9Q34.3) MUTATED	2	1	23	9
AMP PEAK 25(9Q34.3) WILD-TYPE	139	59	100	197

Figure S177. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S178. Gene #26: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 26(10Q22.2) MUTATED	66	45	8	4	20
AMP PEAK 26(10Q22.2) WILD-TYPE	103	260	11	5	17

Figure S178. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S179. Gene #27: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 27(11P11.2) MUTATED	43	1	4	0	3
AMP PEAK 27(11P11.2) WILD-TYPE	126	304	15	9	34

Figure S179. Get High-res Image Gene #27: '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 = 0.012

Table S180. Gene #27: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 27(11P11.2) MUTATED	30	9	4
AMP PEAK 27(11P11.2) WILD-TYPE	135	80	167

Figure S180. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S181. Gene #27: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 27(11P11.2) MUTATED	3	41	6
AMP PEAK 27(11P11.2) WILD-TYPE	148	189	143

Figure S181. Get High-res Image Gene #27: '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 = 0.012

Table S182. Gene #27: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 27(11P11.2) MUTATED	8	36	6
AMP PEAK 27(11P11.2) WILD-TYPE	208	133	139

Figure S182. Get High-res Image Gene #27: '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 = 0.012

Table S183. Gene #27: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 27(11P11.2) MUTATED	41	3	6
AMP PEAK 27(11P11.2) WILD-TYPE	185	140	155

Figure S183. Get High-res Image Gene #27: '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 = 0.012

Table S184. Gene #27: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 27(11P11.2) MUTATED	4	2	31	13
AMP PEAK 27(11P11.2) WILD-TYPE	137	58	92	193

Figure S184. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S185. Gene #28: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 28(11Q13.2) MUTATED	59	5	5	0	5
AMP PEAK 28(11Q13.2) WILD-TYPE	110	300	14	9	32

Figure S185. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S186. Gene #28: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 28(11Q13.2) MUTATED	43	8	12
AMP PEAK 28(11Q13.2) WILD-TYPE	122	81	159

Figure S186. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S187. Gene #28: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 28(11Q13.2) MUTATED	5	53	15
AMP PEAK 28(11Q13.2) WILD-TYPE	146	177	134

Figure S187. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S188. Gene #28: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 28(11Q13.2) MUTATED	17	41	15
AMP PEAK 28(11Q13.2) WILD-TYPE	199	128	130

Figure S188. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S189. Gene #28: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 28(11Q13.2) MUTATED	48	9	15
AMP PEAK 28(11Q13.2) WILD-TYPE	178	134	146

Figure S189. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S190. Gene #28: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 28(11Q13.2) MUTATED	12	2	34	24
AMP PEAK 28(11Q13.2) WILD-TYPE	129	58	89	182

Figure S190. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S191. Gene #29: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 29(11Q14.1) MUTATED	47	3	4	0	5
AMP PEAK 29(11Q14.1) WILD-TYPE	122	302	15	9	32

Figure S191. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S192. Gene #29: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 29(11Q14.1) MUTATED	35	7	8
AMP PEAK 29(11Q14.1) WILD-TYPE	130	82	163

Figure S192. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S193. Gene #29: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 29(11Q14.1) MUTATED	5	44	9
AMP PEAK 29(11Q14.1) WILD-TYPE	146	186	140

Figure S193. Get High-res Image Gene #29: '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 = 0.012

Table S194. Gene #29: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 29(11Q14.1) MUTATED	12	37	9
AMP PEAK 29(11Q14.1) WILD-TYPE	204	132	136

Figure S194. Get High-res Image Gene #29: '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 = 0.016

Table S195. Gene #29: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 29(11Q14.1) MUTATED	41	6	12
AMP PEAK 29(11Q14.1) WILD-TYPE	185	137	149

Figure S195. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S196. Gene #29: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 29(11Q14.1) MUTATED	8	2	29	20
AMP PEAK 29(11Q14.1) WILD-TYPE	133	58	94	186

Figure S196. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S197. Gene #30: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 30(12P12.1) MUTATED	61	16	7	3	6
AMP PEAK 30(12P12.1) WILD-TYPE	108	289	12	6	31

Figure S197. Get High-res Image Gene #30: '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 = 0.012

Table S198. Gene #30: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 30(12P12.1) MUTATED	55	12	10
AMP PEAK 30(12P12.1) WILD-TYPE	110	77	161

Figure S198. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S199. Gene #30: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 30(12P12.1) MUTATED	12	67	11
AMP PEAK 30(12P12.1) WILD-TYPE	139	163	138

Figure S199. Get High-res Image Gene #30: '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 = 0.012

Table S200. Gene #30: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 30(12P12.1) MUTATED	22	56	12
AMP PEAK 30(12P12.1) WILD-TYPE	194	113	133

Figure S200. Get High-res Image Gene #30: '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 = 0.012

Table S201. Gene #30: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 30(12P12.1) MUTATED	65	16	12
AMP PEAK 30(12P12.1) WILD-TYPE	161	127	149

Figure S201. Get High-res Image Gene #30: '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 = 0.012

Table S202. Gene #30: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 30(12P12.1) MUTATED	13	6	46	28
AMP PEAK 30(12P12.1) WILD-TYPE	128	54	77	178

Figure S202. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.2

Table S203. Gene #30: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 30(12P12.1) MUTATED	47	13	14
AMP PEAK 30(12P12.1) WILD-TYPE	125	83	116

Figure S203. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S204. Gene #30: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 30(12P12.1) MUTATED	44	10	20
AMP PEAK 30(12P12.1) WILD-TYPE	100	105	119

Figure S204. Get High-res Image Gene #30: '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 = 0.012

Table S205. Gene #31: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 31(12Q13.11) MUTATED	59	13	7	3	5
AMP PEAK 31(12Q13.11) WILD-TYPE	110	292	12	6	32

Figure S205. Get High-res Image Gene #31: '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 = 0.012

Table S206. Gene #31: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 31(12Q13.11) MUTATED	49	15	7
AMP PEAK 31(12Q13.11) WILD-TYPE	116	74	164

Figure S206. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S207. Gene #31: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 31(12Q13.11) MUTATED	9	66	10
AMP PEAK 31(12Q13.11) WILD-TYPE	142	164	139

Figure S207. Get High-res Image Gene #31: '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 = 0.012

Table S208. Gene #31: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 31(12Q13.11) MUTATED	18	57	10
AMP PEAK 31(12Q13.11) WILD-TYPE	198	112	135

Figure S208. Get High-res Image Gene #31: '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 = 0.012

Table S209. Gene #31: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 31(12Q13.11) MUTATED	64	12	11
AMP PEAK 31(12Q13.11) WILD-TYPE	162	131	150

Figure S209. Get High-res Image Gene #31: '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 = 0.012

Table S210. Gene #31: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 31(12Q13.11) MUTATED	12	4	47	24
AMP PEAK 31(12Q13.11) WILD-TYPE	129	56	76	182

Figure S210. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.2

Table S211. Gene #31: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 31(12Q13.11) MUTATED	37	9	20
AMP PEAK 31(12Q13.11) WILD-TYPE	107	106	119

Figure S211. Get High-res Image Gene #31: '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 = 0.012

Table S212. Gene #32: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 32(12Q13.2) MUTATED	68	16	6	3	7
AMP PEAK 32(12Q13.2) WILD-TYPE	101	289	13	6	30

Figure S212. Get High-res Image Gene #32: '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 = 0.012

Table S213. Gene #32: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 32(12Q13.2) MUTATED	55	14	13
AMP PEAK 32(12Q13.2) WILD-TYPE	110	75	158

Figure S213. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S214. Gene #32: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 32(12Q13.2) MUTATED	9	74	14
AMP PEAK 32(12Q13.2) WILD-TYPE	142	156	135

Figure S214. Get High-res Image Gene #32: '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 = 0.012

Table S215. Gene #32: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 32(12Q13.2) MUTATED	22	61	14
AMP PEAK 32(12Q13.2) WILD-TYPE	194	108	131

Figure S215. Get High-res Image Gene #32: '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 = 0.012

Table S216. Gene #32: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 32(12Q13.2) MUTATED	71	13	14
AMP PEAK 32(12Q13.2) WILD-TYPE	155	130	147

Figure S216. Get High-res Image Gene #32: '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 = 0.012

Table S217. Gene #32: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 32(12Q13.2) MUTATED	15	4	52	27
AMP PEAK 32(12Q13.2) WILD-TYPE	126	56	71	179

Figure S217. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S218. Gene #32: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 32(12Q13.2) MUTATED	53	12	13
AMP PEAK 32(12Q13.2) WILD-TYPE	119	84	117

Figure S218. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.12

Table S219. Gene #32: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 32(12Q13.2) MUTATED	44	13	21
AMP PEAK 32(12Q13.2) WILD-TYPE	100	102	118

Figure S219. Get High-res Image Gene #32: '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 = 0.012

Table S220. Gene #33: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 33(13Q34) MUTATED	52	3	0	1	2
AMP PEAK 33(13Q34) WILD-TYPE	117	302	19	8	35

Figure S220. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S221. Gene #33: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 33(13Q34) MUTATED	38	11	4
AMP PEAK 33(13Q34) WILD-TYPE	127	78	167

Figure S221. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S222. Gene #33: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 33(13Q34) MUTATED	3	52	3
AMP PEAK 33(13Q34) WILD-TYPE	148	178	146

Figure S222. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S223. Gene #33: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 33(13Q34) MUTATED	5	51	2
AMP PEAK 33(13Q34) WILD-TYPE	211	118	143

Figure S223. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S224. Gene #33: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 33(13Q34) MUTATED	52	2	4
AMP PEAK 33(13Q34) WILD-TYPE	174	141	157

Figure S224. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S225. Gene #33: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 33(13Q34) MUTATED	5	0	40	13
AMP PEAK 33(13Q34) WILD-TYPE	136	60	83	193

Figure S225. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.21

Table S226. Gene #33: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 33(13Q34) MUTATED	33	13	6
AMP PEAK 33(13Q34) WILD-TYPE	139	83	124

Figure S226. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S227. Gene #33: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 33(13Q34) MUTATED	32	3	17
AMP PEAK 33(13Q34) WILD-TYPE	112	112	122

Figure S227. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S228. Gene #34: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 34(14Q24.3) MUTATED	52	4	2	0	6
AMP PEAK 34(14Q24.3) WILD-TYPE	117	301	17	9	31

Figure S228. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q24.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S229. Gene #34: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 34(14Q24.3) MUTATED	37	9	8
AMP PEAK 34(14Q24.3) WILD-TYPE	128	80	163

Figure S229. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S230. Gene #34: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 34(14Q24.3) MUTATED	1	54	7
AMP PEAK 34(14Q24.3) WILD-TYPE	150	176	142

Figure S230. Get High-res Image Gene #34: '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 = 0.012

Table S231. Gene #34: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 34(14Q24.3) MUTATED	7	48	7
AMP PEAK 34(14Q24.3) WILD-TYPE	209	121	138

Figure S231. Get High-res Image Gene #34: '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 = 0.012

Table S232. Gene #34: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 34(14Q24.3) MUTATED	46	7	9
AMP PEAK 34(14Q24.3) WILD-TYPE	180	136	152

Figure S232. Get High-res Image Gene #34: '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 = 0.012

Table S233. Gene #34: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 34(14Q24.3) MUTATED	9	2	36	15
AMP PEAK 34(14Q24.3) WILD-TYPE	132	58	87	191

Figure S233. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S234. Gene #35: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 35(14Q32.33) MUTATED	67	4	2	0	6
AMP PEAK 35(14Q32.33) WILD-TYPE	102	301	17	9	31

Figure S234. Get High-res Image Gene #35: '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 = 0.012

Table S235. Gene #35: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 35(14Q32.33) MUTATED	48	11	9
AMP PEAK 35(14Q32.33) WILD-TYPE	117	78	162

Figure S235. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S236. Gene #35: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 35(14Q32.33) MUTATED	2	60	13
AMP PEAK 35(14Q32.33) WILD-TYPE	149	170	136

Figure S236. Get High-res Image Gene #35: '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 = 0.012

Table S237. Gene #35: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 35(14Q32.33) MUTATED	13	49	13
AMP PEAK 35(14Q32.33) WILD-TYPE	203	120	132

Figure S237. Get High-res Image Gene #35: '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 = 0.012

Table S238. Gene #35: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 35(14Q32.33) MUTATED	57	7	14
AMP PEAK 35(14Q32.33) WILD-TYPE	169	136	147

Figure S238. Get High-res Image Gene #35: '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 = 0.012

Table S239. Gene #35: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 35(14Q32.33) MUTATED	11	2	42	23
AMP PEAK 35(14Q32.33) WILD-TYPE	130	58	81	183

Figure S239. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S240. Gene #36: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 36(15Q26.3) MUTATED	33	2	1	0	2
AMP PEAK 36(15Q26.3) WILD-TYPE	136	303	18	9	35

Figure S240. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S241. Gene #36: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 36(15Q26.3) MUTATED	3	32	3
AMP PEAK 36(15Q26.3) WILD-TYPE	148	198	146

Figure S241. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S242. Gene #36: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 36(15Q26.3) MUTATED	9	26	3
AMP PEAK 36(15Q26.3) WILD-TYPE	207	143	142

Figure S242. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S243. Gene #36: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 36(15Q26.3) MUTATED	30	5	3
AMP PEAK 36(15Q26.3) WILD-TYPE	196	138	158

Figure S243. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S244. Gene #36: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 36(15Q26.3) MUTATED	4	1	21	12
AMP PEAK 36(15Q26.3) WILD-TYPE	137	59	102	194

Figure S244. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S245. Gene #37: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 37(16P11.2) MUTATED	61	1	1	0	3
AMP PEAK 37(16P11.2) WILD-TYPE	108	304	18	9	34

Figure S245. Get High-res Image Gene #37: '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 = 0.012

Table S246. Gene #37: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 37(16P11.2) MUTATED	39	10	8
AMP PEAK 37(16P11.2) WILD-TYPE	126	79	163

Figure S246. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S247. Gene #37: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 37(16P11.2) MUTATED	5	57	4
AMP PEAK 37(16P11.2) WILD-TYPE	146	173	145

Figure S247. Get High-res Image Gene #37: '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 = 0.012

Table S248. Gene #37: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 37(16P11.2) MUTATED	12	50	4
AMP PEAK 37(16P11.2) WILD-TYPE	204	119	141

Figure S248. Get High-res Image Gene #37: '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 = 0.012

Table S249. Gene #37: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 37(16P11.2) MUTATED	52	6	5
AMP PEAK 37(16P11.2) WILD-TYPE	174	137	156

Figure S249. Get High-res Image Gene #37: '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 = 0.012

Table S250. Gene #37: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 37(16P11.2) MUTATED	5	3	39	16
AMP PEAK 37(16P11.2) WILD-TYPE	136	57	84	190

Figure S250. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.21

Table S251. Gene #37: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 37(16P11.2) MUTATED	29	5	18
AMP PEAK 37(16P11.2) WILD-TYPE	115	110	121

Figure S251. Get High-res Image Gene #37: '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 = 0.012

Table S252. Gene #38: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 38(17Q11.2) MUTATED	64	4	0	1	2
AMP PEAK 38(17Q11.2) WILD-TYPE	105	301	19	8	35

Figure S252. Get High-res Image Gene #38: '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 = 0.012

Table S253. Gene #38: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 38(17Q11.2) MUTATED	54	6	3
AMP PEAK 38(17Q11.2) WILD-TYPE	111	83	168

Figure S253. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S254. Gene #38: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 38(17Q11.2) MUTATED	2	63	4
AMP PEAK 38(17Q11.2) WILD-TYPE	149	167	145

Figure S254. Get High-res Image Gene #38: '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 = 0.012

Table S255. Gene #38: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 38(17Q11.2) MUTATED	8	58	3
AMP PEAK 38(17Q11.2) WILD-TYPE	208	111	142

Figure S255. Get High-res Image Gene #38: '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 = 0.012

Table S256. Gene #38: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 38(17Q11.2) MUTATED	58	8	2
AMP PEAK 38(17Q11.2) WILD-TYPE	168	135	159

Figure S256. Get High-res Image Gene #38: '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 = 0.012

Table S257. Gene #38: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 38(17Q11.2) MUTATED	4	1	46	17
AMP PEAK 38(17Q11.2) WILD-TYPE	137	59	77	189

Figure S257. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S258. Gene #38: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 38(17Q11.2) MUTATED	41	12	5
AMP PEAK 38(17Q11.2) WILD-TYPE	131	84	125

Figure S258. Get High-res Image Gene #38: '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 = 0.012

Table S259. Gene #38: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 38(17Q11.2) MUTATED	37	5	16
AMP PEAK 38(17Q11.2) WILD-TYPE	107	110	123

Figure S259. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S260. Gene #39: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 39(17Q12) MUTATED	67	5	0	1	2
AMP PEAK 39(17Q12) WILD-TYPE	102	300	19	8	35

Figure S260. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S261. Gene #39: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 39(17Q12) MUTATED	53	8	2
AMP PEAK 39(17Q12) WILD-TYPE	112	81	169

Figure S261. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S262. Gene #39: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 39(17Q12) MUTATED	2	68	3
AMP PEAK 39(17Q12) WILD-TYPE	149	162	146

Figure S262. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S263. Gene #39: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 39(17Q12) MUTATED	7	64	2
AMP PEAK 39(17Q12) WILD-TYPE	209	105	143

Figure S263. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S264. Gene #39: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 39(17Q12) MUTATED	66	4	3
AMP PEAK 39(17Q12) WILD-TYPE	160	139	158

Figure S264. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S265. Gene #39: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 39(17Q12) MUTATED	4	2	53	14
AMP PEAK 39(17Q12) WILD-TYPE	137	58	70	192

Figure S265. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S266. Gene #39: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 39(17Q12) MUTATED	40	13	7
AMP PEAK 39(17Q12) WILD-TYPE	132	83	123

Figure S266. Get High-res Image Gene #39: '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 = 0.012

Table S267. Gene #39: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 39(17Q12) MUTATED	37	3	20
AMP PEAK 39(17Q12) WILD-TYPE	107	112	119

Figure S267. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S268. Gene #40: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 40(17Q25.1) MUTATED	0	10	1	0
AMP PEAK 40(17Q25.1) WILD-TYPE	14	7	11	10

Figure S268. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S269. Gene #40: '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 40(17Q25.1) MUTATED	2	8	1	0	0
AMP PEAK 40(17Q25.1) WILD-TYPE	12	1	6	7	16

Figure S269. Get High-res Image Gene #40: '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 = 0.012

Table S270. Gene #40: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 40(17Q25.1) MUTATED	94	5	1	1	4
AMP PEAK 40(17Q25.1) WILD-TYPE	75	300	18	8	33

Figure S270. Get High-res Image Gene #40: '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 = 0.012

Table S271. Gene #40: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 40(17Q25.1) MUTATED	64	15	6
AMP PEAK 40(17Q25.1) WILD-TYPE	101	74	165

Figure S271. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S272. Gene #40: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 40(17Q25.1) MUTATED	5	88	9
AMP PEAK 40(17Q25.1) WILD-TYPE	146	142	140

Figure S272. Get High-res Image Gene #40: '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 = 0.012

Table S273. Gene #40: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 40(17Q25.1) MUTATED	12	82	8
AMP PEAK 40(17Q25.1) WILD-TYPE	204	87	137

Figure S273. Get High-res Image Gene #40: '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 = 0.012

Table S274. Gene #40: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 40(17Q25.1) MUTATED	84	9	8
AMP PEAK 40(17Q25.1) WILD-TYPE	142	134	153

Figure S274. Get High-res Image Gene #40: '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 = 0.012

Table S275. Gene #40: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 40(17Q25.1) MUTATED	7	2	63	29
AMP PEAK 40(17Q25.1) WILD-TYPE	134	58	60	177

Figure S275. Get High-res Image Gene #40: '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 = 0.012

Table S276. Gene #40: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 40(17Q25.1) MUTATED	53	21	7
AMP PEAK 40(17Q25.1) WILD-TYPE	119	75	123

Figure S276. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S277. Gene #40: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 40(17Q25.1) MUTATED	42	9	30
AMP PEAK 40(17Q25.1) WILD-TYPE	102	106	109

Figure S277. Get High-res Image Gene #40: '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 = 0.012

Table S278. Gene #41: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 41(18P11.31) MUTATED	87	5	3	0	1
AMP PEAK 41(18P11.31) WILD-TYPE	82	300	16	9	36

Figure S278. Get High-res Image Gene #41: '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 = 0.012

Table S279. Gene #41: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 41(18P11.31) MUTATED	62	16	7
AMP PEAK 41(18P11.31) WILD-TYPE	103	73	164

Figure S279. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S280. Gene #41: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 41(18P11.31) MUTATED	3	84	8
AMP PEAK 41(18P11.31) WILD-TYPE	148	146	141

Figure S280. Get High-res Image Gene #41: '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 = 0.012

Table S281. Gene #41: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 41(18P11.31) MUTATED	10	77	8
AMP PEAK 41(18P11.31) WILD-TYPE	206	92	137

Figure S281. Get High-res Image Gene #41: '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 = 0.012

Table S282. Gene #41: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 41(18P11.31) MUTATED	81	7	7
AMP PEAK 41(18P11.31) WILD-TYPE	145	136	154

Figure S282. Get High-res Image Gene #41: '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 = 0.012

Table S283. Gene #41: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 41(18P11.31) MUTATED	9	1	64	21
AMP PEAK 41(18P11.31) WILD-TYPE	132	59	59	185

Figure S283. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S284. Gene #41: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 41(18P11.31) MUTATED	52	23	7
AMP PEAK 41(18P11.31) WILD-TYPE	120	73	123

Figure S284. Get High-res Image Gene #41: '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 = 0.012

Table S285. Gene #41: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 41(18P11.31) MUTATED	46	6	30
AMP PEAK 41(18P11.31) WILD-TYPE	98	109	109

Figure S285. Get High-res Image Gene #41: '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 = 0.012

Table S286. Gene #42: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 42(18Q11.2) MUTATED	63	3	2	0	1
AMP PEAK 42(18Q11.2) WILD-TYPE	106	302	17	9	36

Figure S286. Get High-res Image Gene #42: '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 = 0.012

Table S287. Gene #42: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 42(18Q11.2) MUTATED	47	11	3
AMP PEAK 42(18Q11.2) WILD-TYPE	118	78	168

Figure S287. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S288. Gene #42: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 42(18Q11.2) MUTATED	3	62	3
AMP PEAK 42(18Q11.2) WILD-TYPE	148	168	146

Figure S288. Get High-res Image Gene #42: '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 = 0.012

Table S289. Gene #42: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 42(18Q11.2) MUTATED	8	57	3
AMP PEAK 42(18Q11.2) WILD-TYPE	208	112	142

Figure S289. Get High-res Image Gene #42: '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 = 0.012

Table S290. Gene #42: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 42(18Q11.2) MUTATED	59	7	2
AMP PEAK 42(18Q11.2) WILD-TYPE	167	136	159

Figure S290. Get High-res Image Gene #42: '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 = 0.012

Table S291. Gene #42: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 42(18Q11.2) MUTATED	3	1	44	20
AMP PEAK 42(18Q11.2) WILD-TYPE	138	59	79	186

Figure S291. Get High-res Image Gene #42: '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 = 0.012

Table S292. Gene #42: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 42(18Q11.2) MUTATED	43	13	1
AMP PEAK 42(18Q11.2) WILD-TYPE	129	83	129

Figure S292. Get High-res Image Gene #42: '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 = 0.012

Table S293. Gene #42: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 42(18Q11.2) MUTATED	35	1	21
AMP PEAK 42(18Q11.2) WILD-TYPE	109	114	118

Figure S293. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.049

Table S294. Gene #43: '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 43(19P13.2) MUTATED	2	6	0	0	0
AMP PEAK 43(19P13.2) WILD-TYPE	12	3	7	7	16

Figure S294. Get High-res Image Gene #43: '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 = 0.012

Table S295. Gene #43: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 43(19P13.2) MUTATED	95	0	1	0	3
AMP PEAK 43(19P13.2) WILD-TYPE	74	305	18	9	34

Figure S295. Get High-res Image Gene #43: '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 = 0.012

Table S296. Gene #43: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 43(19P13.2) MUTATED	65	15	7
AMP PEAK 43(19P13.2) WILD-TYPE	100	74	164

Figure S296. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.21

Table S297. Gene #43: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
AMP PEAK 43(19P13.2) MUTATED	13	3	0	4
AMP PEAK 43(19P13.2) WILD-TYPE	54	64	43	13

Figure S297. Get High-res Image Gene #43: '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 = 0.012

Table S298. Gene #43: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 43(19P13.2) MUTATED	2	89	6
AMP PEAK 43(19P13.2) WILD-TYPE	149	141	143

Figure S298. Get High-res Image Gene #43: '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 = 0.012

Table S299. Gene #43: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 43(19P13.2) MUTATED	11	81	5
AMP PEAK 43(19P13.2) WILD-TYPE	205	88	140

Figure S299. Get High-res Image Gene #43: '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 = 0.012

Table S300. Gene #43: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 43(19P13.2) MUTATED	84	7	6
AMP PEAK 43(19P13.2) WILD-TYPE	142	136	155

Figure S300. Get High-res Image Gene #43: '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 = 0.012

Table S301. Gene #43: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 43(19P13.2) MUTATED	9	1	63	24
AMP PEAK 43(19P13.2) WILD-TYPE	132	59	60	182

Figure S301. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S302. Gene #43: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 43(19P13.2) MUTATED	51	22	8
AMP PEAK 43(19P13.2) WILD-TYPE	121	74	122

Figure S302. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S303. Gene #43: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 43(19P13.2) MUTATED	47	8	26
AMP PEAK 43(19P13.2) WILD-TYPE	97	107	113

Figure S303. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S304. Gene #44: '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 44(19Q12) MUTATED	2	7	1	0	0
AMP PEAK 44(19Q12) WILD-TYPE	12	2	6	7	16

Figure S304. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S305. Gene #44: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 44(19Q12) MUTATED	113	2	2	0	4
AMP PEAK 44(19Q12) WILD-TYPE	56	303	17	9	33

Figure S305. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S306. Gene #44: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 44(19Q12) MUTATED	80	18	9
AMP PEAK 44(19Q12) WILD-TYPE	85	71	162

Figure S306. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S307. Gene #44: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 44(19Q12) MUTATED	3	109	7
AMP PEAK 44(19Q12) WILD-TYPE	148	121	142

Figure S307. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S308. Gene #44: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 44(19Q12) MUTATED	15	98	6
AMP PEAK 44(19Q12) WILD-TYPE	201	71	139

Figure S308. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S309. Gene #44: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 44(19Q12) MUTATED	101	8	8
AMP PEAK 44(19Q12) WILD-TYPE	125	135	153

Figure S309. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S310. Gene #44: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 44(19Q12) MUTATED	10	1	78	28
AMP PEAK 44(19Q12) WILD-TYPE	131	59	45	178

Figure S310. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S311. Gene #44: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 44(19Q12) MUTATED	66	27	8
AMP PEAK 44(19Q12) WILD-TYPE	106	69	122

Figure S311. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S312. Gene #44: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 44(19Q12) MUTATED	56	10	35
AMP PEAK 44(19Q12) WILD-TYPE	88	105	104

Figure S312. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S313. Gene #45: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 45(20P13) MUTATED	87	8	12	2	8
AMP PEAK 45(20P13) WILD-TYPE	82	297	7	7	29

Figure S313. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S314. Gene #45: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 45(20P13) MUTATED	75	16	16
AMP PEAK 45(20P13) WILD-TYPE	90	73	155

Figure S314. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S315. Gene #45: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 45(20P13) MUTATED	11	89	15
AMP PEAK 45(20P13) WILD-TYPE	140	141	134

Figure S315. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S316. Gene #45: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 45(20P13) MUTATED	18	80	17
AMP PEAK 45(20P13) WILD-TYPE	198	89	128

Figure S316. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S317. Gene #45: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 45(20P13) MUTATED	86	15	15
AMP PEAK 45(20P13) WILD-TYPE	140	128	146

Figure S317. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S318. Gene #45: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 45(20P13) MUTATED	13	7	59	37
AMP PEAK 45(20P13) WILD-TYPE	128	53	64	169

Figure S318. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.22

Table S319. Gene #45: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 45(20P13) MUTATED	57	23	18
AMP PEAK 45(20P13) WILD-TYPE	115	73	112

Figure S319. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S320. Gene #45: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 45(20P13) MUTATED	56	13	29
AMP PEAK 45(20P13) WILD-TYPE	88	102	110

Figure S320. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.18

Table S321. Gene #46: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 46(20Q11.21) MUTATED	2	9	0	0
AMP PEAK 46(20Q11.21) WILD-TYPE	12	8	12	10

Figure S321. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S322. Gene #46: '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 46(20Q11.21) MUTATED	4	7	0	0	0
AMP PEAK 46(20Q11.21) WILD-TYPE	10	2	7	7	16

Figure S322. Get High-res Image Gene #46: '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 = 0.012

Table S323. Gene #46: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 46(20Q11.21) MUTATED	120	8	13	3	8
AMP PEAK 46(20Q11.21) WILD-TYPE	49	297	6	6	29

Figure S323. Get High-res Image Gene #46: '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 = 0.012

Table S324. Gene #46: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 46(20Q11.21) MUTATED	89	20	24
AMP PEAK 46(20Q11.21) WILD-TYPE	76	69	147

Figure S324. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.18

Table S325. Gene #46: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
AMP PEAK 46(20Q11.21) MUTATED	8	12	2	0	2	8
AMP PEAK 46(20Q11.21) WILD-TYPE	33	25	37	12	39	16

Figure S325. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S326. Gene #46: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 46(20Q11.21) MUTATED	11	118	21
AMP PEAK 46(20Q11.21) WILD-TYPE	140	112	128

Figure S326. Get High-res Image Gene #46: '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 = 0.012

Table S327. Gene #46: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 46(20Q11.21) MUTATED	26	101	23
AMP PEAK 46(20Q11.21) WILD-TYPE	190	68	122

Figure S327. Get High-res Image Gene #46: '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 = 0.012

Table S328. Gene #46: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 46(20Q11.21) MUTATED	110	17	21
AMP PEAK 46(20Q11.21) WILD-TYPE	116	126	140

Figure S328. Get High-res Image Gene #46: '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 = 0.012

Table S329. Gene #46: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 46(20Q11.21) MUTATED	21	7	80	40
AMP PEAK 46(20Q11.21) WILD-TYPE	120	53	43	166

Figure S329. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S330. Gene #46: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 46(20Q11.21) MUTATED	76	26	23
AMP PEAK 46(20Q11.21) WILD-TYPE	96	70	107

Figure S330. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S331. Gene #46: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 46(20Q11.21) MUTATED	69	22	34
AMP PEAK 46(20Q11.21) WILD-TYPE	75	93	105

Figure S331. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S332. Gene #47: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 47(20Q13.12) MUTATED	118	10	14	3	7
AMP PEAK 47(20Q13.12) WILD-TYPE	51	295	5	6	30

Figure S332. Get High-res Image Gene #47: '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 = 0.012

Table S333. Gene #47: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 47(20Q13.12) MUTATED	94	20	24
AMP PEAK 47(20Q13.12) WILD-TYPE	71	69	147

Figure S333. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S334. Gene #47: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 47(20Q13.12) MUTATED	12	117	20
AMP PEAK 47(20Q13.12) WILD-TYPE	139	113	129

Figure S334. Get High-res Image Gene #47: '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 = 0.012

Table S335. Gene #47: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 47(20Q13.12) MUTATED	26	102	21
AMP PEAK 47(20Q13.12) WILD-TYPE	190	67	124

Figure S335. Get High-res Image Gene #47: '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 = 0.012

Table S336. Gene #47: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 47(20Q13.12) MUTATED	112	18	21
AMP PEAK 47(20Q13.12) WILD-TYPE	114	125	140

Figure S336. Get High-res Image Gene #47: '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 = 0.012

Table S337. Gene #47: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 47(20Q13.12) MUTATED	21	7	79	44
AMP PEAK 47(20Q13.12) WILD-TYPE	120	53	44	162

Figure S337. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S338. Gene #47: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 47(20Q13.12) MUTATED	77	28	24
AMP PEAK 47(20Q13.12) WILD-TYPE	95	68	106

Figure S338. Get High-res Image Gene #47: '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 = 0.012

Table S339. Gene #47: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 47(20Q13.12) MUTATED	74	21	34
AMP PEAK 47(20Q13.12) WILD-TYPE	70	94	105

Figure S339. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S340. Gene #48: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 48(20Q13.33) MUTATED	117	11	15	3	7
AMP PEAK 48(20Q13.33) WILD-TYPE	52	294	4	6	30

Figure S340. Get High-res Image Gene #48: '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 = 0.012

Table S341. Gene #48: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 48(20Q13.33) MUTATED	91	21	24
AMP PEAK 48(20Q13.33) WILD-TYPE	74	68	147

Figure S341. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S342. Gene #48: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 48(20Q13.33) MUTATED	14	116	21
AMP PEAK 48(20Q13.33) WILD-TYPE	137	114	128

Figure S342. Get High-res Image Gene #48: '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 = 0.012

Table S343. Gene #48: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 48(20Q13.33) MUTATED	29	100	22
AMP PEAK 48(20Q13.33) WILD-TYPE	187	69	123

Figure S343. Get High-res Image Gene #48: '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 = 0.012

Table S344. Gene #48: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 48(20Q13.33) MUTATED	110	18	22
AMP PEAK 48(20Q13.33) WILD-TYPE	116	125	139

Figure S344. Get High-res Image Gene #48: '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 = 0.012

Table S345. Gene #48: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 48(20Q13.33) MUTATED	21	8	77	44
AMP PEAK 48(20Q13.33) WILD-TYPE	120	52	46	162

Figure S345. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S346. Gene #48: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 48(20Q13.33) MUTATED	76	28	23
AMP PEAK 48(20Q13.33) WILD-TYPE	96	68	107

Figure S346. Get High-res Image Gene #48: '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 = 0.012

Table S347. Gene #48: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 48(20Q13.33) MUTATED	71	21	35
AMP PEAK 48(20Q13.33) WILD-TYPE	73	94	104

Figure S347. Get High-res Image Gene #48: '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 = 0.012

Table S348. Gene #49: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 49(22Q12.2) MUTATED	56	4	1	1	0
AMP PEAK 49(22Q12.2) WILD-TYPE	113	301	18	8	37

Figure S348. Get High-res Image Gene #49: '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 = 0.012

Table S349. Gene #49: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 49(22Q12.2) MUTATED	49	8	0
AMP PEAK 49(22Q12.2) WILD-TYPE	116	81	171

Figure S349. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S350. Gene #49: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 49(22Q12.2) MUTATED	1	60	0
AMP PEAK 49(22Q12.2) WILD-TYPE	150	170	149

Figure S350. Get High-res Image Gene #49: '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 = 0.012

Table S351. Gene #49: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 49(22Q12.2) MUTATED	3	58	0
AMP PEAK 49(22Q12.2) WILD-TYPE	213	111	145

Figure S351. Get High-res Image Gene #49: '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 = 0.012

Table S352. Gene #49: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
AMP PEAK 49(22Q12.2) MUTATED	60	1	0
AMP PEAK 49(22Q12.2) WILD-TYPE	166	142	161

Figure S352. Get High-res Image Gene #49: '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 = 0.012

Table S353. Gene #49: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 49(22Q12.2) MUTATED	1	1	46	13
AMP PEAK 49(22Q12.2) WILD-TYPE	140	59	77	193

Figure S353. Get High-res Image Gene #49: '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 = 0.012

Table S354. Gene #49: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 49(22Q12.2) MUTATED	43	10	3
AMP PEAK 49(22Q12.2) WILD-TYPE	129	86	127

Figure S354. Get High-res Image Gene #49: '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 = 0.012

Table S355. Gene #49: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 49(22Q12.2) MUTATED	40	1	15
AMP PEAK 49(22Q12.2) WILD-TYPE	104	114	124

Figure S355. Get High-res Image Gene #49: '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 = 0.012

Table S356. Gene #50: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 50(XP11.23) MUTATED	48	8	8	3	23
AMP PEAK 50(XP11.23) WILD-TYPE	121	297	11	6	14

Figure S356. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.1

Table S357. Gene #50: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 50(XP11.23) MUTATED	43	11	17
AMP PEAK 50(XP11.23) WILD-TYPE	122	78	154

Figure S357. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S358. Gene #50: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
AMP PEAK 50(XP11.23) MUTATED	15	56	17
AMP PEAK 50(XP11.23) WILD-TYPE	136	174	132

Figure S358. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S359. Gene #50: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 50(XP11.23) MUTATED	23	48	17
AMP PEAK 50(XP11.23) WILD-TYPE	193	121	128

Figure S359. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.22

Table S360. Gene #50: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
AMP PEAK 50(XP11.23) MUTATED	16	6	36	31
AMP PEAK 50(XP11.23) WILD-TYPE	125	54	87	175

Figure S360. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S361. Gene #51: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 51(XQ28) MUTATED	49	10	8	3	23
AMP PEAK 51(XQ28) WILD-TYPE	120	295	11	6	14

Figure S361. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.059

Table S362. Gene #51: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
AMP PEAK 51(XQ28) MUTATED	27	47	17
AMP PEAK 51(XQ28) WILD-TYPE	189	122	128

Figure S362. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S363. Gene #52: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 1(1P36.21) MUTATED	60	3	3	5	0
DEL PEAK 1(1P36.21) WILD-TYPE	109	302	16	4	37

Figure S363. Get High-res Image Gene #52: '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 = 0.012

Table S364. Gene #52: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 1(1P36.21) MUTATED	39	15	6
DEL PEAK 1(1P36.21) WILD-TYPE	126	74	165

Figure S364. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S365. Gene #52: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 1(1P36.21) MUTATED	6	60	4
DEL PEAK 1(1P36.21) WILD-TYPE	145	170	145

Figure S365. Get High-res Image Gene #52: '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 = 0.012

Table S366. Gene #52: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 1(1P36.21) MUTATED	17	50	3
DEL PEAK 1(1P36.21) WILD-TYPE	199	119	142

Figure S366. Get High-res Image Gene #52: '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 = 0.012

Table S367. Gene #52: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 1(1P36.21) MUTATED	54	8	6
DEL PEAK 1(1P36.21) WILD-TYPE	172	135	155

Figure S367. Get High-res Image Gene #52: '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 = 0.012

Table S368. Gene #52: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 1(1P36.21) MUTATED	3	0	40	25
DEL PEAK 1(1P36.21) WILD-TYPE	138	60	83	181

Figure S368. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.099

Table S369. Gene #52: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 1(1P36.21) MUTATED	27	5	28
DEL PEAK 1(1P36.21) WILD-TYPE	117	110	111

Figure S369. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S370. Gene #53: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 2(1P36.11) MUTATED	72	2	4	5	0
DEL PEAK 2(1P36.11) WILD-TYPE	97	303	15	4	37

Figure S370. Get High-res Image Gene #53: '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 = 0.012

Table S371. Gene #53: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 2(1P36.11) MUTATED	56	12	6
DEL PEAK 2(1P36.11) WILD-TYPE	109	77	165

Figure S371. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S372. Gene #53: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 2(1P36.11) MUTATED	6	72	4
DEL PEAK 2(1P36.11) WILD-TYPE	145	158	145

Figure S372. Get High-res Image Gene #53: '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 = 0.012

Table S373. Gene #53: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 2(1P36.11) MUTATED	19	60	3
DEL PEAK 2(1P36.11) WILD-TYPE	197	109	142

Figure S373. Get High-res Image Gene #53: '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 = 0.012

Table S374. Gene #53: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 2(1P36.11) MUTATED	66	7	7
DEL PEAK 2(1P36.11) WILD-TYPE	160	136	154

Figure S374. Get High-res Image Gene #53: '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 = 0.012

Table S375. Gene #53: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 2(1P36.11) MUTATED	3	0	47	30
DEL PEAK 2(1P36.11) WILD-TYPE	138	60	76	176

Figure S375. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S376. Gene #53: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 2(1P36.11) MUTATED	42	6	25
DEL PEAK 2(1P36.11) WILD-TYPE	102	109	114

Figure S376. Get High-res Image Gene #53: '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 = 0.012

Table S377. Gene #54: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 3(2P25.3) MUTATED	24	2	0	0	0
DEL PEAK 3(2P25.3) WILD-TYPE	145	303	19	9	37

Figure S377. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.081

Table S378. Gene #54: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 3(2P25.3) MUTATED	19	4	2
DEL PEAK 3(2P25.3) WILD-TYPE	146	85	169

Figure S378. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S379. Gene #54: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 3(2P25.3) MUTATED	1	22	3
DEL PEAK 3(2P25.3) WILD-TYPE	150	208	146

Figure S379. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S380. Gene #54: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 3(2P25.3) MUTATED	4	19	3
DEL PEAK 3(2P25.3) WILD-TYPE	212	150	142

Figure S380. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.19

Table S381. Gene #54: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 3(2P25.3) MUTATED	21	2	3
DEL PEAK 3(2P25.3) WILD-TYPE	205	141	158

Figure S381. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S382. Gene #55: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 4(2Q22.1) MUTATED	46	0	2	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	123	305	17	9	37

Figure S382. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S383. Gene #55: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 4(2Q22.1) MUTATED	30	8	4
DEL PEAK 4(2Q22.1) WILD-TYPE	135	81	167

Figure S383. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S384. Gene #55: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 4(2Q22.1) MUTATED	0	43	5
DEL PEAK 4(2Q22.1) WILD-TYPE	151	187	144

Figure S384. Get High-res Image Gene #55: '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 = 0.012

Table S385. Gene #55: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 4(2Q22.1) MUTATED	8	34	6
DEL PEAK 4(2Q22.1) WILD-TYPE	208	135	139

Figure S385. Get High-res Image Gene #55: '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 = 0.012

Table S386. Gene #55: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 4(2Q22.1) MUTATED	37	5	4
DEL PEAK 4(2Q22.1) WILD-TYPE	189	138	157

Figure S386. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.045

Table S387. Gene #55: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 4(2Q22.1) MUTATED	5	1	22	18
DEL PEAK 4(2Q22.1) WILD-TYPE	136	59	101	188

Figure S387. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S388. Gene #56: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 5(2Q37.3) MUTATED	49	1	2	0	1
DEL PEAK 5(2Q37.3) WILD-TYPE	120	304	17	9	36

Figure S388. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S389. Gene #56: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 5(2Q37.3) MUTATED	35	6	8
DEL PEAK 5(2Q37.3) WILD-TYPE	130	83	163

Figure S389. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S390. Gene #56: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 5(2Q37.3) MUTATED	3	42	7
DEL PEAK 5(2Q37.3) WILD-TYPE	148	188	142

Figure S390. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S391. Gene #56: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 5(2Q37.3) MUTATED	13	32	7
DEL PEAK 5(2Q37.3) WILD-TYPE	203	137	138

Figure S391. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S392. Gene #56: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 5(2Q37.3) MUTATED	39	5	8
DEL PEAK 5(2Q37.3) WILD-TYPE	187	138	153

Figure S392. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S393. Gene #57: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 6(3P14.2) MUTATED	72	0	4	2	1
DEL PEAK 6(3P14.2) WILD-TYPE	97	305	15	7	36

Figure S393. Get High-res Image Gene #57: '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 = 0.012

Table S394. Gene #57: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 6(3P14.2) MUTATED	51	12	5
DEL PEAK 6(3P14.2) WILD-TYPE	114	77	166

Figure S394. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S395. Gene #57: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 6(3P14.2) MUTATED	1	71	4
DEL PEAK 6(3P14.2) WILD-TYPE	150	159	145

Figure S395. Get High-res Image Gene #57: '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 = 0.012

Table S396. Gene #57: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 6(3P14.2) MUTATED	13	58	5
DEL PEAK 6(3P14.2) WILD-TYPE	203	111	140

Figure S396. Get High-res Image Gene #57: '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 = 0.012

Table S397. Gene #57: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 6(3P14.2) MUTATED	64	9	4
DEL PEAK 6(3P14.2) WILD-TYPE	162	134	157

Figure S397. Get High-res Image Gene #57: '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 = 0.012

Table S398. Gene #57: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 6(3P14.2) MUTATED	6	2	43	26
DEL PEAK 6(3P14.2) WILD-TYPE	135	58	80	180

Figure S398. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.13

Table S399. Gene #57: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 6(3P14.2) MUTATED	41	16	9
DEL PEAK 6(3P14.2) WILD-TYPE	131	80	121

Figure S399. Get High-res Image Gene #57: '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 = 0.012

Table S400. Gene #57: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 6(3P14.2) MUTATED	42	4	20
DEL PEAK 6(3P14.2) WILD-TYPE	102	111	119

Figure S400. Get High-res Image Gene #57: '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 = 0.012

Table S401. Gene #58: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 7(3Q13.31) MUTATED	36	4	0	2	1
DEL PEAK 7(3Q13.31) WILD-TYPE	133	301	19	7	36

Figure S401. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.21

Table S402. Gene #58: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 7(3Q13.31) MUTATED	24	7	5
DEL PEAK 7(3Q13.31) WILD-TYPE	141	82	166

Figure S402. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S403. Gene #58: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 7(3Q13.31) MUTATED	2	35	6
DEL PEAK 7(3Q13.31) WILD-TYPE	149	195	143

Figure S403. Get High-res Image Gene #58: '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 = 0.012

Table S404. Gene #58: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 7(3Q13.31) MUTATED	5	32	6
DEL PEAK 7(3Q13.31) WILD-TYPE	211	137	139

Figure S404. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S405. Gene #58: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 7(3Q13.31) MUTATED	32	4	5
DEL PEAK 7(3Q13.31) WILD-TYPE	194	139	156

Figure S405. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.21

Table S406. Gene #58: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 7(3Q13.31) MUTATED	5	2	21	13
DEL PEAK 7(3Q13.31) WILD-TYPE	136	58	102	193

Figure S406. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S407. Gene #59: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 8(4P16.3) MUTATED	79	4	5	4	2
DEL PEAK 8(4P16.3) WILD-TYPE	90	301	14	5	35

Figure S407. Get High-res Image Gene #59: '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 = 0.012

Table S408. Gene #59: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 8(4P16.3) MUTATED	62	13	7
DEL PEAK 8(4P16.3) WILD-TYPE	103	76	164

Figure S408. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S409. Gene #59: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 8(4P16.3) MUTATED	6	78	9
DEL PEAK 8(4P16.3) WILD-TYPE	145	152	140

Figure S409. Get High-res Image Gene #59: '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 = 0.012

Table S410. Gene #59: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 8(4P16.3) MUTATED	18	68	7
DEL PEAK 8(4P16.3) WILD-TYPE	198	101	138

Figure S410. Get High-res Image Gene #59: '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 = 0.012

Table S411. Gene #59: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 8(4P16.3) MUTATED	73	9	9
DEL PEAK 8(4P16.3) WILD-TYPE	153	134	152

Figure S411. Get High-res Image Gene #59: '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 = 0.012

Table S412. Gene #59: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 8(4P16.3) MUTATED	6	1	55	29
DEL PEAK 8(4P16.3) WILD-TYPE	135	59	68	177

Figure S412. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S413. Gene #59: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 8(4P16.3) MUTATED	46	24	10
DEL PEAK 8(4P16.3) WILD-TYPE	126	72	120

Figure S413. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S414. Gene #59: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 8(4P16.3) MUTATED	45	8	27
DEL PEAK 8(4P16.3) WILD-TYPE	99	107	112

Figure S414. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S415. Gene #60: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 9(4P15.2) MUTATED	84	3	5	4	2
DEL PEAK 9(4P15.2) WILD-TYPE	85	302	14	5	35

Figure S415. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S416. Gene #60: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 9(4P15.2) MUTATED	67	14	6
DEL PEAK 9(4P15.2) WILD-TYPE	98	75	165

Figure S416. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S417. Gene #60: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 9(4P15.2) MUTATED	6	83	8
DEL PEAK 9(4P15.2) WILD-TYPE	145	147	141

Figure S417. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S418. Gene #60: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 9(4P15.2) MUTATED	20	70	7
DEL PEAK 9(4P15.2) WILD-TYPE	196	99	138

Figure S418. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S419. Gene #60: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 9(4P15.2) MUTATED	78	10	8
DEL PEAK 9(4P15.2) WILD-TYPE	148	133	153

Figure S419. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S420. Gene #60: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 9(4P15.2) MUTATED	5	1	58	32
DEL PEAK 9(4P15.2) WILD-TYPE	136	59	65	174

Figure S420. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S421. Gene #60: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 9(4P15.2) MUTATED	52	24	10
DEL PEAK 9(4P15.2) WILD-TYPE	120	72	120

Figure S421. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S422. Gene #60: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 9(4P15.2) MUTATED	49	7	30
DEL PEAK 9(4P15.2) WILD-TYPE	95	108	109

Figure S422. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.049

Table S423. Gene #61: '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 S423. Get High-res Image Gene #61: '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 = 0.012

Table S424. Gene #61: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 10(4Q22.1) MUTATED	94	2	4	4	2
DEL PEAK 10(4Q22.1) WILD-TYPE	75	303	15	5	35

Figure S424. Get High-res Image Gene #61: '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 = 0.012

Table S425. Gene #61: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 10(4Q22.1) MUTATED	71	16	5
DEL PEAK 10(4Q22.1) WILD-TYPE	94	73	166

Figure S425. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S426. Gene #61: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 10(4Q22.1) MUTATED	5	93	7
DEL PEAK 10(4Q22.1) WILD-TYPE	146	137	142

Figure S426. Get High-res Image Gene #61: '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 = 0.012

Table S427. Gene #61: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 10(4Q22.1) MUTATED	20	79	6
DEL PEAK 10(4Q22.1) WILD-TYPE	196	90	139

Figure S427. Get High-res Image Gene #61: '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 = 0.012

Table S428. Gene #61: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 10(4Q22.1) MUTATED	88	8	7
DEL PEAK 10(4Q22.1) WILD-TYPE	138	135	154

Figure S428. Get High-res Image Gene #61: '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 = 0.012

Table S429. Gene #61: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 10(4Q22.1) MUTATED	4	0	66	33
DEL PEAK 10(4Q22.1) WILD-TYPE	137	60	57	173

Figure S429. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S430. Gene #61: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 10(4Q22.1) MUTATED	56	26	8
DEL PEAK 10(4Q22.1) WILD-TYPE	116	70	122

Figure S430. Get High-res Image Gene #61: '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 = 0.012

Table S431. Gene #61: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 10(4Q22.1) MUTATED	48	5	37
DEL PEAK 10(4Q22.1) WILD-TYPE	96	110	102

Figure S431. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.054

Table S432. Gene #62: '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 S432. Get High-res Image Gene #62: '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 = 0.012

Table S433. Gene #62: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 11(4Q34.3) MUTATED	111	6	6	4	3
DEL PEAK 11(4Q34.3) WILD-TYPE	58	299	13	5	34

Figure S433. Get High-res Image Gene #62: '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 = 0.012

Table S434. Gene #62: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 11(4Q34.3) MUTATED	81	22	11
DEL PEAK 11(4Q34.3) WILD-TYPE	84	67	160

Figure S434. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S435. Gene #62: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 11(4Q34.3) MUTATED	8	113	8
DEL PEAK 11(4Q34.3) WILD-TYPE	143	117	141

Figure S435. Get High-res Image Gene #62: '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 = 0.012

Table S436. Gene #62: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 11(4Q34.3) MUTATED	27	95	7
DEL PEAK 11(4Q34.3) WILD-TYPE	189	74	138

Figure S436. Get High-res Image Gene #62: '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 = 0.012

Table S437. Gene #62: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 11(4Q34.3) MUTATED	102	17	8
DEL PEAK 11(4Q34.3) WILD-TYPE	124	126	153

Figure S437. Get High-res Image Gene #62: '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 = 0.012

Table S438. Gene #62: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 11(4Q34.3) MUTATED	7	1	74	45
DEL PEAK 11(4Q34.3) WILD-TYPE	134	59	49	161

Figure S438. Get High-res Image Gene #62: '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 = 0.012

Table S439. Gene #62: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 11(4Q34.3) MUTATED	66	33	13
DEL PEAK 11(4Q34.3) WILD-TYPE	106	63	117

Figure S439. Get High-res Image Gene #62: '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 = 0.012

Table S440. Gene #62: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 11(4Q34.3) MUTATED	59	7	46
DEL PEAK 11(4Q34.3) WILD-TYPE	85	108	93

Figure S440. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S441. Gene #63: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 12(5Q12.1) MUTATED	103	0	2	2	4
DEL PEAK 12(5Q12.1) WILD-TYPE	66	305	17	7	33

Figure S441. Get High-res Image Gene #63: '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 = 0.012

Table S442. Gene #63: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 12(5Q12.1) MUTATED	75	14	8
DEL PEAK 12(5Q12.1) WILD-TYPE	90	75	163

Figure S442. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.099

Table S443. Gene #63: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
DEL PEAK 12(5Q12.1) MUTATED	6	9	1	0	0	6
DEL PEAK 12(5Q12.1) WILD-TYPE	35	28	38	12	41	18

Figure S443. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S444. Gene #63: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 12(5Q12.1) MUTATED	4	95	10
DEL PEAK 12(5Q12.1) WILD-TYPE	147	135	139

Figure S444. Get High-res Image Gene #63: '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 = 0.012

Table S445. Gene #63: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 12(5Q12.1) MUTATED	19	79	11
DEL PEAK 12(5Q12.1) WILD-TYPE	197	90	134

Figure S445. Get High-res Image Gene #63: '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 = 0.012

Table S446. Gene #63: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 12(5Q12.1) MUTATED	90	10	10
DEL PEAK 12(5Q12.1) WILD-TYPE	136	133	151

Figure S446. Get High-res Image Gene #63: '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 = 0.012

Table S447. Gene #63: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 12(5Q12.1) MUTATED	9	0	62	39
DEL PEAK 12(5Q12.1) WILD-TYPE	132	60	61	167

Figure S447. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S448. Gene #63: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 12(5Q12.1) MUTATED	61	22	12
DEL PEAK 12(5Q12.1) WILD-TYPE	111	74	118

Figure S448. Get High-res Image Gene #63: '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 = 0.012

Table S449. Gene #63: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 12(5Q12.1) MUTATED	54	10	31
DEL PEAK 12(5Q12.1) WILD-TYPE	90	105	108

Figure S449. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S450. Gene #64: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 13(6Q26) MUTATED	39	4	2	1	0
DEL PEAK 13(6Q26) WILD-TYPE	130	301	17	8	37

Figure S450. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S451. Gene #64: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 13(6Q26) MUTATED	31	8	1
DEL PEAK 13(6Q26) WILD-TYPE	134	81	170

Figure S451. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S452. Gene #64: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 13(6Q26) MUTATED	2	42	2
DEL PEAK 13(6Q26) WILD-TYPE	149	188	147

Figure S452. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S453. Gene #64: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 13(6Q26) MUTATED	6	39	1
DEL PEAK 13(6Q26) WILD-TYPE	210	130	144

Figure S453. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S454. Gene #64: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 13(6Q26) MUTATED	37	6	2
DEL PEAK 13(6Q26) WILD-TYPE	189	137	159

Figure S454. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S455. Gene #64: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 13(6Q26) MUTATED	2	0	28	15
DEL PEAK 13(6Q26) WILD-TYPE	139	60	95	191

Figure S455. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S456. Gene #64: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 13(6Q26) MUTATED	19	1	19
DEL PEAK 13(6Q26) WILD-TYPE	125	114	120

Figure S456. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.068

Table S457. Gene #65: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 14(7P22.3) MUTATED	0	8	0	0
DEL PEAK 14(7P22.3) WILD-TYPE	14	9	12	10

Figure S457. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S458. Gene #65: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 14(7P22.3) MUTATED	65	4	1	1	1
DEL PEAK 14(7P22.3) WILD-TYPE	104	301	18	8	36

Figure S458. Get High-res Image Gene #65: '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 = 0.012

Table S459. Gene #65: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 14(7P22.3) MUTATED	45	13	4
DEL PEAK 14(7P22.3) WILD-TYPE	120	76	167

Figure S459. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S460. Gene #65: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 14(7P22.3) MUTATED	2	66	4
DEL PEAK 14(7P22.3) WILD-TYPE	149	164	145

Figure S460. Get High-res Image Gene #65: '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 = 0.012

Table S461. Gene #65: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 14(7P22.3) MUTATED	8	60	4
DEL PEAK 14(7P22.3) WILD-TYPE	208	109	141

Figure S461. Get High-res Image Gene #65: '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 = 0.012

Table S462. Gene #65: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 14(7P22.3) MUTATED	60	5	5
DEL PEAK 14(7P22.3) WILD-TYPE	166	138	156

Figure S462. Get High-res Image Gene #65: '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 = 0.012

Table S463. Gene #65: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 14(7P22.3) MUTATED	3	0	48	19
DEL PEAK 14(7P22.3) WILD-TYPE	138	60	75	187

Figure S463. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.1

Table S464. Gene #65: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 14(7P22.3) MUTATED	34	18	6
DEL PEAK 14(7P22.3) WILD-TYPE	138	78	124

Figure S464. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S465. Gene #65: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 14(7P22.3) MUTATED	33	4	21
DEL PEAK 14(7P22.3) WILD-TYPE	111	111	118

Figure S465. Get High-res Image Gene #65: '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 = 0.012

Table S466. Gene #66: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 15(7Q11.22) MUTATED	39	0	0	1	1
DEL PEAK 15(7Q11.22) WILD-TYPE	130	305	19	8	36

Figure S466. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S467. Gene #66: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 15(7Q11.22) MUTATED	27	8	3
DEL PEAK 15(7Q11.22) WILD-TYPE	138	81	168

Figure S467. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S468. Gene #66: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 15(7Q11.22) MUTATED	0	39	2
DEL PEAK 15(7Q11.22) WILD-TYPE	151	191	147

Figure S468. Get High-res Image Gene #66: '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 = 0.012

Table S469. Gene #66: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 15(7Q11.22) MUTATED	7	31	3
DEL PEAK 15(7Q11.22) WILD-TYPE	209	138	142

Figure S469. Get High-res Image Gene #66: '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 = 0.012

Table S470. Gene #66: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 15(7Q11.22) MUTATED	34	3	3
DEL PEAK 15(7Q11.22) WILD-TYPE	192	140	158

Figure S470. Get High-res Image Gene #66: '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 = 0.012

Table S471. Gene #66: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 15(7Q11.22) MUTATED	3	0	26	11
DEL PEAK 15(7Q11.22) WILD-TYPE	138	60	97	195

Figure S471. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S472. Gene #67: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 16(7Q31.1) MUTATED	54	0	0	1	0
DEL PEAK 16(7Q31.1) WILD-TYPE	115	305	19	8	37

Figure S472. Get High-res Image Gene #67: '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 = 0.012

Table S473. Gene #67: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 16(7Q31.1) MUTATED	38	11	1
DEL PEAK 16(7Q31.1) WILD-TYPE	127	78	170

Figure S473. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S474. Gene #67: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 16(7Q31.1) MUTATED	0	54	1
DEL PEAK 16(7Q31.1) WILD-TYPE	151	176	148

Figure S474. Get High-res Image Gene #67: '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 = 0.012

Table S475. Gene #67: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 16(7Q31.1) MUTATED	5	48	2
DEL PEAK 16(7Q31.1) WILD-TYPE	211	121	143

Figure S475. Get High-res Image Gene #67: '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 = 0.012

Table S476. Gene #67: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 16(7Q31.1) MUTATED	49	2	3
DEL PEAK 16(7Q31.1) WILD-TYPE	177	141	158

Figure S476. Get High-res Image Gene #67: '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 = 0.012

Table S477. Gene #67: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 16(7Q31.1) MUTATED	3	0	41	10
DEL PEAK 16(7Q31.1) WILD-TYPE	138	60	82	196

Figure S477. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.15

Table S478. Gene #67: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 16(7Q31.1) MUTATED	32	10	5
DEL PEAK 16(7Q31.1) WILD-TYPE	140	86	125

Figure S478. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.23

Table S479. Gene #67: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 16(7Q31.1) MUTATED	27	4	16
DEL PEAK 16(7Q31.1) WILD-TYPE	117	111	123

Figure S479. Get High-res Image Gene #67: '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 = 0.012

Table S480. Gene #68: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 17(7Q36.1) MUTATED	60	1	0	1	1
DEL PEAK 17(7Q36.1) WILD-TYPE	109	304	19	8	36

Figure S480. Get High-res Image Gene #68: '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 = 0.012

Table S481. Gene #68: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 17(7Q36.1) MUTATED	41	12	1
DEL PEAK 17(7Q36.1) WILD-TYPE	124	77	170

Figure S481. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S482. Gene #68: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 17(7Q36.1) MUTATED	0	62	1
DEL PEAK 17(7Q36.1) WILD-TYPE	151	168	148

Figure S482. Get High-res Image Gene #68: '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 = 0.012

Table S483. Gene #68: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 17(7Q36.1) MUTATED	4	57	2
DEL PEAK 17(7Q36.1) WILD-TYPE	212	112	143

Figure S483. Get High-res Image Gene #68: '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 = 0.012

Table S484. Gene #68: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 17(7Q36.1) MUTATED	57	2	3
DEL PEAK 17(7Q36.1) WILD-TYPE	169	141	158

Figure S484. Get High-res Image Gene #68: '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 = 0.012

Table S485. Gene #68: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 17(7Q36.1) MUTATED	3	0	47	12
DEL PEAK 17(7Q36.1) WILD-TYPE	138	60	76	194

Figure S485. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.059

Table S486. Gene #68: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 17(7Q36.1) MUTATED	34	11	5
DEL PEAK 17(7Q36.1) WILD-TYPE	138	85	125

Figure S486. Get High-res Image Gene #68: '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 = 0.016

Table S487. Gene #68: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 17(7Q36.1) MUTATED	31	3	16
DEL PEAK 17(7Q36.1) WILD-TYPE	113	112	123

Figure S487. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S488. Gene #69: '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 S488. Get High-res Image Gene #69: '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 = 0.012

Table S489. Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 18(8P23.2) MUTATED	107	7	4	1	0
DEL PEAK 18(8P23.2) WILD-TYPE	62	298	15	8	37

Figure S489. Get High-res Image Gene #69: '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 = 0.012

Table S490. Gene #69: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 18(8P23.2) MUTATED	84	16	5
DEL PEAK 18(8P23.2) WILD-TYPE	81	73	166

Figure S490. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S491. Gene #69: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 18(8P23.2) MUTATED	5	106	5
DEL PEAK 18(8P23.2) WILD-TYPE	146	124	144

Figure S491. Get High-res Image Gene #69: '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 = 0.012

Table S492. Gene #69: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 18(8P23.2) MUTATED	16	94	6
DEL PEAK 18(8P23.2) WILD-TYPE	200	75	139

Figure S492. Get High-res Image Gene #69: '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 = 0.012

Table S493. Gene #69: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 18(8P23.2) MUTATED	104	5	7
DEL PEAK 18(8P23.2) WILD-TYPE	122	138	154

Figure S493. Get High-res Image Gene #69: '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 = 0.012

Table S494. Gene #69: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 18(8P23.2) MUTATED	6	1	75	34
DEL PEAK 18(8P23.2) WILD-TYPE	135	59	48	172

Figure S494. Get High-res Image Gene #69: '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 = 0.012

Table S495. Gene #69: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 18(8P23.2) MUTATED	68	22	9
DEL PEAK 18(8P23.2) WILD-TYPE	104	74	121

Figure S495. Get High-res Image Gene #69: '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 = 0.012

Table S496. Gene #69: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 18(8P23.2) MUTATED	61	4	34
DEL PEAK 18(8P23.2) WILD-TYPE	83	111	105

Figure S496. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S497. Gene #70: '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 S497. Get High-res Image Gene #70: '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 = 0.012

Table S498. Gene #70: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 19(8P21.2) MUTATED	109	4	3	1	0
DEL PEAK 19(8P21.2) WILD-TYPE	60	301	16	8	37

Figure S498. Get High-res Image Gene #70: '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 = 0.012

Table S499. Gene #70: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 19(8P21.2) MUTATED	86	15	2
DEL PEAK 19(8P21.2) WILD-TYPE	79	74	169

Figure S499. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S500. Gene #70: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 19(8P21.2) MUTATED	4	108	2
DEL PEAK 19(8P21.2) WILD-TYPE	147	122	147

Figure S500. Get High-res Image Gene #70: '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 = 0.012

Table S501. Gene #70: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 19(8P21.2) MUTATED	14	97	3
DEL PEAK 19(8P21.2) WILD-TYPE	202	72	142

Figure S501. Get High-res Image Gene #70: '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 = 0.012

Table S502. Gene #70: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 19(8P21.2) MUTATED	106	5	3
DEL PEAK 19(8P21.2) WILD-TYPE	120	138	158

Figure S502. Get High-res Image Gene #70: '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 = 0.012

Table S503. Gene #70: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 19(8P21.2) MUTATED	3	1	80	30
DEL PEAK 19(8P21.2) WILD-TYPE	138	59	43	176

Figure S503. Get High-res Image Gene #70: '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 = 0.012

Table S504. Gene #70: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 19(8P21.2) MUTATED	68	23	7
DEL PEAK 19(8P21.2) WILD-TYPE	104	73	123

Figure S504. Get High-res Image Gene #70: '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 = 0.012

Table S505. Gene #70: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 19(8P21.2) MUTATED	62	2	34
DEL PEAK 19(8P21.2) WILD-TYPE	82	113	105

Figure S505. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S506. Gene #71: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 20(9P23) MUTATED	67	2	5	1	4
DEL PEAK 20(9P23) WILD-TYPE	102	303	14	8	33

Figure S506. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S507. Gene #71: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 20(9P23) MUTATED	44	18	8
DEL PEAK 20(9P23) WILD-TYPE	121	71	163

Figure S507. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S508. Gene #71: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 20(9P23) MUTATED	5	62	11
DEL PEAK 20(9P23) WILD-TYPE	146	168	138

Figure S508. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S509. Gene #71: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 20(9P23) MUTATED	13	54	11
DEL PEAK 20(9P23) WILD-TYPE	203	115	134

Figure S509. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S510. Gene #71: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 20(9P23) MUTATED	57	7	14
DEL PEAK 20(9P23) WILD-TYPE	169	136	147

Figure S510. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S511. Gene #71: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 20(9P23) MUTATED	11	1	47	19
DEL PEAK 20(9P23) WILD-TYPE	130	59	76	187

Figure S511. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.03

Table S512. Gene #72: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 21(9Q21.2) MUTATED	0	9	0	0
DEL PEAK 21(9Q21.2) WILD-TYPE	14	8	12	10

Figure S512. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S513. Gene #72: '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 S513. Get High-res Image Gene #72: '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 = 0.012

Table S514. Gene #72: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 21(9Q21.2) MUTATED	112	3	7	2	5
DEL PEAK 21(9Q21.2) WILD-TYPE	57	302	12	7	32

Figure S514. Get High-res Image Gene #72: '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 = 0.012

Table S515. Gene #72: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 21(9Q21.2) MUTATED	78	20	15
DEL PEAK 21(9Q21.2) WILD-TYPE	87	69	156

Figure S515. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.2' versus 'RPPA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.16

Table S516. Gene #72: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
DEL PEAK 21(9Q21.2) MUTATED	6	12	1	2	1	6
DEL PEAK 21(9Q21.2) WILD-TYPE	35	25	38	10	40	18

Figure S516. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S517. Gene #72: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 21(9Q21.2) MUTATED	8	103	16
DEL PEAK 21(9Q21.2) WILD-TYPE	143	127	133

Figure S517. Get High-res Image Gene #72: '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 = 0.012

Table S518. Gene #72: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 21(9Q21.2) MUTATED	21	90	16
DEL PEAK 21(9Q21.2) WILD-TYPE	195	79	129

Figure S518. Get High-res Image Gene #72: '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 = 0.012

Table S519. Gene #72: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 21(9Q21.2) MUTATED	96	13	17
DEL PEAK 21(9Q21.2) WILD-TYPE	130	130	144

Figure S519. Get High-res Image Gene #72: '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 = 0.012

Table S520. Gene #72: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 21(9Q21.2) MUTATED	17	2	70	37
DEL PEAK 21(9Q21.2) WILD-TYPE	124	58	53	169

Figure S520. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.17

Table S521. Gene #72: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 21(9Q21.2) MUTATED	61	29	20
DEL PEAK 21(9Q21.2) WILD-TYPE	111	67	110

Figure S521. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S522. Gene #72: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 21(9Q21.2) MUTATED	61	16	33
DEL PEAK 21(9Q21.2) WILD-TYPE	83	99	106

Figure S522. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S523. Gene #73: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 22(9Q34.2) MUTATED	0	9	0	0
DEL PEAK 22(9Q34.2) WILD-TYPE	14	8	12	10

Figure S523. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S524. Gene #73: '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 S524. Get High-res Image Gene #73: '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 = 0.012

Table S525. Gene #73: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 22(9Q34.2) MUTATED	117	4	6	1	4
DEL PEAK 22(9Q34.2) WILD-TYPE	52	301	13	8	33

Figure S525. Get High-res Image Gene #73: '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 = 0.012

Table S526. Gene #73: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 22(9Q34.2) MUTATED	78	23	13
DEL PEAK 22(9Q34.2) WILD-TYPE	87	66	158

Figure S526. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.2

Table S527. Gene #73: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
DEL PEAK 22(9Q34.2) MUTATED	7	13	2	2	1	6
DEL PEAK 22(9Q34.2) WILD-TYPE	34	24	37	10	40	18

Figure S527. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S528. Gene #73: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 22(9Q34.2) MUTATED	8	105	17
DEL PEAK 22(9Q34.2) WILD-TYPE	143	125	132

Figure S528. Get High-res Image Gene #73: '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 = 0.012

Table S529. Gene #73: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 22(9Q34.2) MUTATED	25	89	16
DEL PEAK 22(9Q34.2) WILD-TYPE	191	80	129

Figure S529. Get High-res Image Gene #73: '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 = 0.012

Table S530. Gene #73: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 22(9Q34.2) MUTATED	98	13	18
DEL PEAK 22(9Q34.2) WILD-TYPE	128	130	143

Figure S530. Get High-res Image Gene #73: '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 = 0.012

Table S531. Gene #73: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 22(9Q34.2) MUTATED	17	2	70	40
DEL PEAK 22(9Q34.2) WILD-TYPE	124	58	53	166

Figure S531. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S532. Gene #73: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 22(9Q34.2) MUTATED	64	27	20
DEL PEAK 22(9Q34.2) WILD-TYPE	108	69	110

Figure S532. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S533. Gene #73: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 22(9Q34.2) MUTATED	65	17	29
DEL PEAK 22(9Q34.2) WILD-TYPE	79	98	110

Figure S533. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S534. Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 23(10Q23.31) MUTATED	70	5	2	0	0
DEL PEAK 23(10Q23.31) WILD-TYPE	99	300	17	9	37

Figure S534. 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 = 0.012

Table S535. Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 23(10Q23.31) MUTATED	49	13	6
DEL PEAK 23(10Q23.31) WILD-TYPE	116	76	165

Figure S535. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S536. Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 23(10Q23.31) MUTATED	4	62	8
DEL PEAK 23(10Q23.31) WILD-TYPE	147	168	141

Figure S536. 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 = 0.012

Table S537. Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 23(10Q23.31) MUTATED	14	52	8
DEL PEAK 23(10Q23.31) WILD-TYPE	202	117	137

Figure S537. 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 = 0.012

Table S538. Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 23(10Q23.31) MUTATED	61	7	8
DEL PEAK 23(10Q23.31) WILD-TYPE	165	136	153

Figure S538. 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 = 0.012

Table S539. Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 23(10Q23.31) MUTATED	9	1	42	24
DEL PEAK 23(10Q23.31) WILD-TYPE	132	59	81	182

Figure S539. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S540. Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 23(10Q23.31) MUTATED	41	7	19
DEL PEAK 23(10Q23.31) WILD-TYPE	103	108	120

Figure S540. 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 = 0.012

Table S541. Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 24(11P15.5) MUTATED	94	1	6	4	1
DEL PEAK 24(11P15.5) WILD-TYPE	75	304	13	5	36

Figure S541. 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 = 0.012

Table S542. Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 24(11P15.5) MUTATED	74	17	6
DEL PEAK 24(11P15.5) WILD-TYPE	91	72	165

Figure S542. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S543. Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 24(11P15.5) MUTATED	3	88	12
DEL PEAK 24(11P15.5) WILD-TYPE	148	142	137

Figure S543. 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 = 0.012

Table S544. Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 24(11P15.5) MUTATED	15	76	12
DEL PEAK 24(11P15.5) WILD-TYPE	201	93	133

Figure S544. 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 = 0.012

Table S545. Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 24(11P15.5) MUTATED	84	8	13
DEL PEAK 24(11P15.5) WILD-TYPE	142	135	148

Figure S545. 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 = 0.012

Table S546. Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 24(11P15.5) MUTATED	13	1	64	27
DEL PEAK 24(11P15.5) WILD-TYPE	128	59	59	179

Figure S546. 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 = 0.012

Table S547. Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 24(11P15.5) MUTATED	66	18	13
DEL PEAK 24(11P15.5) WILD-TYPE	106	78	117

Figure S547. 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 = 0.012

Table S548. Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 24(11P15.5) MUTATED	62	12	23
DEL PEAK 24(11P15.5) WILD-TYPE	82	103	116

Figure S548. 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 = 0.012

Table S549. Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 25(11Q14.1) MUTATED	61	0	4	4	1
DEL PEAK 25(11Q14.1) WILD-TYPE	108	305	15	5	36

Figure S549. 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 = 0.012

Table S550. Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 25(11Q14.1) MUTATED	51	10	5
DEL PEAK 25(11Q14.1) WILD-TYPE	114	79	166

Figure S550. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S551. Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 25(11Q14.1) MUTATED	2	59	7
DEL PEAK 25(11Q14.1) WILD-TYPE	149	171	142

Figure S551. 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 = 0.012

Table S552. Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 25(11Q14.1) MUTATED	8	54	6
DEL PEAK 25(11Q14.1) WILD-TYPE	208	115	139

Figure S552. 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 = 0.012

Table S553. Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 25(11Q14.1) MUTATED	56	6	8
DEL PEAK 25(11Q14.1) WILD-TYPE	170	137	153

Figure S553. 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 = 0.012

Table S554. Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 25(11Q14.1) MUTATED	6	0	46	18
DEL PEAK 25(11Q14.1) WILD-TYPE	135	60	77	188

Figure S554. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S555. Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 25(11Q14.1) MUTATED	46	12	7
DEL PEAK 25(11Q14.1) WILD-TYPE	126	84	123

Figure S555. 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 = 0.012

Table S556. Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 25(11Q14.1) MUTATED	42	6	17
DEL PEAK 25(11Q14.1) WILD-TYPE	102	109	122

Figure S556. 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 = 0.012

Table S557. Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 26(11Q25) MUTATED	77	3	6	4	3
DEL PEAK 26(11Q25) WILD-TYPE	92	302	13	5	34

Figure S557. 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 = 0.012

Table S558. Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 26(11Q25) MUTATED	66	11	7
DEL PEAK 26(11Q25) WILD-TYPE	99	78	164

Figure S558. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S559. Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 26(11Q25) MUTATED	6	75	10
DEL PEAK 26(11Q25) WILD-TYPE	145	155	139

Figure S559. 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 = 0.012

Table S560. Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 26(11Q25) MUTATED	17	65	9
DEL PEAK 26(11Q25) WILD-TYPE	199	104	136

Figure S560. 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 = 0.012

Table S561. Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 26(11Q25) MUTATED	68	11	12
DEL PEAK 26(11Q25) WILD-TYPE	158	132	149

Figure S561. 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 = 0.012

Table S562. Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 26(11Q25) MUTATED	7	1	52	31
DEL PEAK 26(11Q25) WILD-TYPE	134	59	71	175

Figure S562. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S563. Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 26(11Q25) MUTATED	53	18	11
DEL PEAK 26(11Q25) WILD-TYPE	119	78	119

Figure S563. 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 = 0.012

Table S564. Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 26(11Q25) MUTATED	49	8	25
DEL PEAK 26(11Q25) WILD-TYPE	95	107	114

Figure S564. 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 = 0.012

Table S565. Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 27(12Q23.1) MUTATED	54	0	1	0	1
DEL PEAK 27(12Q23.1) WILD-TYPE	115	305	18	9	36

Figure S565. 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 = 0.012

Table S566. Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 27(12Q23.1) MUTATED	42	6	0
DEL PEAK 27(12Q23.1) WILD-TYPE	123	83	171

Figure S566. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S567. Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 27(12Q23.1) MUTATED	1	50	4
DEL PEAK 27(12Q23.1) WILD-TYPE	150	180	145

Figure S567. 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 = 0.012

Table S568. Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 27(12Q23.1) MUTATED	3	47	5
DEL PEAK 27(12Q23.1) WILD-TYPE	213	122	140

Figure S568. 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 = 0.012

Table S569. Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 27(12Q23.1) MUTATED	46	6	2
DEL PEAK 27(12Q23.1) WILD-TYPE	180	137	159

Figure S569. 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 = 0.012

Table S570. Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 27(12Q23.1) MUTATED	0	1	37	16
DEL PEAK 27(12Q23.1) WILD-TYPE	141	59	86	190

Figure S570. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S571. Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 27(12Q23.1) MUTATED	32	11	4
DEL PEAK 27(12Q23.1) WILD-TYPE	140	85	126

Figure S571. 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 = 1e-05 (Fisher's exact test), Q value = 0.012

Table S572. Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 27(12Q23.1) MUTATED	30	2	15
DEL PEAK 27(12Q23.1) WILD-TYPE	114	113	124

Figure S572. 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 = 0.012

Table S573. Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 28(12Q24.33) MUTATED	63	1	1	0	1
DEL PEAK 28(12Q24.33) WILD-TYPE	106	304	18	9	36

Figure S573. 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 = 0.012

Table S574. Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 28(12Q24.33) MUTATED	50	8	3
DEL PEAK 28(12Q24.33) WILD-TYPE	115	81	168

Figure S574. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S575. Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 28(12Q24.33) MUTATED	1	61	3
DEL PEAK 28(12Q24.33) WILD-TYPE	150	169	146

Figure S575. 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 = 0.012

Table S576. Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 28(12Q24.33) MUTATED	9	52	4
DEL PEAK 28(12Q24.33) WILD-TYPE	207	117	141

Figure S576. 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 = 0.012

Table S577. Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 28(12Q24.33) MUTATED	55	6	3
DEL PEAK 28(12Q24.33) WILD-TYPE	171	137	158

Figure S577. 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 = 0.012

Table S578. Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 28(12Q24.33) MUTATED	2	1	39	22
DEL PEAK 28(12Q24.33) WILD-TYPE	139	59	84	184

Figure S578. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S579. Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 28(12Q24.33) MUTATED	40	12	7
DEL PEAK 28(12Q24.33) WILD-TYPE	132	84	123

Figure S579. 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 = 0.012

Table S580. Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 28(12Q24.33) MUTATED	37	4	18
DEL PEAK 28(12Q24.33) WILD-TYPE	107	111	121

Figure S580. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S581. Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 29(13Q11) MUTATED	80	3	6	3	6
DEL PEAK 29(13Q11) WILD-TYPE	89	302	13	6	31

Figure S581. 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 = 0.012

Table S582. Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 29(13Q11) MUTATED	57	17	10
DEL PEAK 29(13Q11) WILD-TYPE	108	72	161

Figure S582. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S583. Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 29(13Q11) MUTATED	6	75	16
DEL PEAK 29(13Q11) WILD-TYPE	145	155	133

Figure S583. 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 = 0.012

Table S584. Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 29(13Q11) MUTATED	21	61	15
DEL PEAK 29(13Q11) WILD-TYPE	195	108	130

Figure S584. 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 = 0.012

Table S585. Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 29(13Q11) MUTATED	71	13	13
DEL PEAK 29(13Q11) WILD-TYPE	155	130	148

Figure S585. 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 = 0.012

Table S586. Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 29(13Q11) MUTATED	12	2	48	35
DEL PEAK 29(13Q11) WILD-TYPE	129	58	75	171

Figure S586. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S587. Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 30(13Q14.2) MUTATED	86	5	8	3	5
DEL PEAK 30(13Q14.2) WILD-TYPE	83	300	11	6	32

Figure S587. 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 = 0.012

Table S588. Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 30(13Q14.2) MUTATED	60	20	14
DEL PEAK 30(13Q14.2) WILD-TYPE	105	69	157

Figure S588. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S589. Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 30(13Q14.2) MUTATED	7	78	19
DEL PEAK 30(13Q14.2) WILD-TYPE	144	152	130

Figure S589. 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 = 0.012

Table S590. Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 30(13Q14.2) MUTATED	26	60	18
DEL PEAK 30(13Q14.2) WILD-TYPE	190	109	127

Figure S590. 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 = 0.012

Table S591. Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 30(13Q14.2) MUTATED	72	17	17
DEL PEAK 30(13Q14.2) WILD-TYPE	154	126	144

Figure S591. 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 = 0.012

Table S592. Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 30(13Q14.2) MUTATED	15	4	47	40
DEL PEAK 30(13Q14.2) WILD-TYPE	126	56	76	166

Figure S592. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S593. Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 31(14Q13.1) MUTATED	63	2	2	3	3
DEL PEAK 31(14Q13.1) WILD-TYPE	106	303	17	6	34

Figure S593. 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 = 0.012

Table S594. Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 31(14Q13.1) MUTATED	51	8	5
DEL PEAK 31(14Q13.1) WILD-TYPE	114	81	166

Figure S594. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S595. Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 31(14Q13.1) MUTATED	4	61	6
DEL PEAK 31(14Q13.1) WILD-TYPE	147	169	143

Figure S595. 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 = 0.012

Table S596. Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 31(14Q13.1) MUTATED	11	54	6
DEL PEAK 31(14Q13.1) WILD-TYPE	205	115	139

Figure S596. 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 = 0.012

Table S597. Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 31(14Q13.1) MUTATED	58	10	4
DEL PEAK 31(14Q13.1) WILD-TYPE	168	133	157

Figure S597. 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 = 0.012

Table S598. Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 31(14Q13.1) MUTATED	4	1	44	23
DEL PEAK 31(14Q13.1) WILD-TYPE	137	59	79	183

Figure S598. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S599. Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 31(14Q13.1) MUTATED	38	5	21
DEL PEAK 31(14Q13.1) WILD-TYPE	106	110	118

Figure S599. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S600. Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 32(15Q15.1) MUTATED	119	5	8	5	3
DEL PEAK 32(15Q15.1) WILD-TYPE	50	300	11	4	34

Figure S600. 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 = 0.012

Table S601. Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 32(15Q15.1) MUTATED	90	23	12
DEL PEAK 32(15Q15.1) WILD-TYPE	75	66	159

Figure S601. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S602. Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 32(15Q15.1) MUTATED	9	119	12
DEL PEAK 32(15Q15.1) WILD-TYPE	142	111	137

Figure S602. 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 = 0.012

Table S603. Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 32(15Q15.1) MUTATED	29	99	12
DEL PEAK 32(15Q15.1) WILD-TYPE	187	70	133

Figure S603. 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 = 0.012

Table S604. Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 32(15Q15.1) MUTATED	112	14	12
DEL PEAK 32(15Q15.1) WILD-TYPE	114	129	149

Figure S604. 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 = 0.012

Table S605. Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 32(15Q15.1) MUTATED	11	2	79	46
DEL PEAK 32(15Q15.1) WILD-TYPE	130	58	44	160

Figure S605. 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 = 0.012

Table S606. Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 32(15Q15.1) MUTATED	70	34	18
DEL PEAK 32(15Q15.1) WILD-TYPE	102	62	112

Figure S606. 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 = 0.012

Table S607. Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 32(15Q15.1) MUTATED	67	12	43
DEL PEAK 32(15Q15.1) WILD-TYPE	77	103	96

Figure S607. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.23

Table S608. 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 33(15Q23) MUTATED	1	5	0	0	0
DEL PEAK 33(15Q23) WILD-TYPE	13	4	7	7	16

Figure S608. 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 = 0.012

Table S609. Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 33(15Q23) MUTATED	95	4	7	6	3
DEL PEAK 33(15Q23) WILD-TYPE	74	301	12	3	34

Figure S609. 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 = 0.012

Table S610. Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 33(15Q23) MUTATED	77	16	8
DEL PEAK 33(15Q23) WILD-TYPE	88	73	163

Figure S610. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S611. Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 33(15Q23) MUTATED	8	97	9
DEL PEAK 33(15Q23) WILD-TYPE	143	133	140

Figure S611. 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 = 0.012

Table S612. Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 33(15Q23) MUTATED	21	85	8
DEL PEAK 33(15Q23) WILD-TYPE	195	84	137

Figure S612. 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 = 0.012

Table S613. Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 33(15Q23) MUTATED	90	14	9
DEL PEAK 33(15Q23) WILD-TYPE	136	129	152

Figure S613. 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 = 0.012

Table S614. Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 33(15Q23) MUTATED	8	2	65	38
DEL PEAK 33(15Q23) WILD-TYPE	133	58	58	168

Figure S614. 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 = 0.012

Table S615. Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 33(15Q23) MUTATED	64	22	12
DEL PEAK 33(15Q23) WILD-TYPE	108	74	118

Figure S615. 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 = 0.012

Table S616. Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 33(15Q23) MUTATED	59	7	32
DEL PEAK 33(15Q23) WILD-TYPE	85	108	107

Figure S616. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S617. Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 34(16P13.3) MUTATED	84	2	3	1	2
DEL PEAK 34(16P13.3) WILD-TYPE	85	303	16	8	35

Figure S617. 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 = 0.012

Table S618. Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 34(16P13.3) MUTATED	62	17	4
DEL PEAK 34(16P13.3) WILD-TYPE	103	72	167

Figure S618. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S619. Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 34(16P13.3) MUTATED	2	82	7
DEL PEAK 34(16P13.3) WILD-TYPE	149	148	142

Figure S619. 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 = 0.012

Table S620. Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 34(16P13.3) MUTATED	13	71	7
DEL PEAK 34(16P13.3) WILD-TYPE	203	98	138

Figure S620. 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 = 0.012

Table S621. Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 34(16P13.3) MUTATED	76	7	7
DEL PEAK 34(16P13.3) WILD-TYPE	150	136	154

Figure S621. 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 = 0.012

Table S622. Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 34(16P13.3) MUTATED	5	1	59	25
DEL PEAK 34(16P13.3) WILD-TYPE	136	59	64	181

Figure S622. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S623. Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 34(16P13.3) MUTATED	51	21	10
DEL PEAK 34(16P13.3) WILD-TYPE	121	75	120

Figure S623. 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 = 0.012

Table S624. Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 34(16P13.3) MUTATED	49	6	27
DEL PEAK 34(16P13.3) WILD-TYPE	95	109	112

Figure S624. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.04

Table S625. 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 35(16Q21) MUTATED	1	7	0	0	1
DEL PEAK 35(16Q21) WILD-TYPE	13	2	7	7	15

Figure S625. 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 = 0.012

Table S626. Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 35(16Q21) MUTATED	128	14	7	1	4
DEL PEAK 35(16Q21) WILD-TYPE	41	291	12	8	33

Figure S626. 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 = 0.012

Table S627. Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 35(16Q21) MUTATED	93	26	16
DEL PEAK 35(16Q21) WILD-TYPE	72	63	155

Figure S627. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S628. Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 35(16Q21) MUTATED	14	123	16
DEL PEAK 35(16Q21) WILD-TYPE	137	107	133

Figure S628. 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 = 0.012

Table S629. Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 35(16Q21) MUTATED	33	105	15
DEL PEAK 35(16Q21) WILD-TYPE	183	64	130

Figure S629. 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 = 0.012

Table S630. Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 35(16Q21) MUTATED	111	22	17
DEL PEAK 35(16Q21) WILD-TYPE	115	121	144

Figure S630. 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 = 0.012

Table S631. Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 35(16Q21) MUTATED	16	7	82	45
DEL PEAK 35(16Q21) WILD-TYPE	125	53	41	161

Figure S631. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S632. Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 35(16Q21) MUTATED	78	31	22
DEL PEAK 35(16Q21) WILD-TYPE	94	65	108

Figure S632. 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 = 0.012

Table S633. Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 35(16Q21) MUTATED	72	16	43
DEL PEAK 35(16Q21) WILD-TYPE	72	99	96

Figure S633. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S634. Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 36(16Q22.3) MUTATED	129	17	7	1	4
DEL PEAK 36(16Q22.3) WILD-TYPE	40	288	12	8	33

Figure S634. 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 = 0.012

Table S635. Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 36(16Q22.3) MUTATED	91	28	19
DEL PEAK 36(16Q22.3) WILD-TYPE	74	61	152

Figure S635. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S636. Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 36(16Q22.3) MUTATED	15	125	18
DEL PEAK 36(16Q22.3) WILD-TYPE	136	105	131

Figure S636. 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 = 0.012

Table S637. Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 36(16Q22.3) MUTATED	36	105	17
DEL PEAK 36(16Q22.3) WILD-TYPE	180	64	128

Figure S637. 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 = 0.012

Table S638. Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 36(16Q22.3) MUTATED	112	23	19
DEL PEAK 36(16Q22.3) WILD-TYPE	114	120	142

Figure S638. 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 = 0.012

Table S639. Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 36(16Q22.3) MUTATED	18	7	84	45
DEL PEAK 36(16Q22.3) WILD-TYPE	123	53	39	161

Figure S639. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S640. Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 36(16Q22.3) MUTATED	75	34	25
DEL PEAK 36(16Q22.3) WILD-TYPE	97	62	105

Figure S640. 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 = 0.012

Table S641. Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 36(16Q22.3) MUTATED	68	16	50
DEL PEAK 36(16Q22.3) WILD-TYPE	76	99	89

Figure S641. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.068

Table S642. 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 37(16Q23.1) MUTATED	4	7	0	0	1
DEL PEAK 37(16Q23.1) WILD-TYPE	10	2	7	7	15

Figure S642. 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 = 0.012

Table S643. Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 37(16Q23.1) MUTATED	134	19	8	1	4
DEL PEAK 37(16Q23.1) WILD-TYPE	35	286	11	8	33

Figure S643. 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 = 0.012

Table S644. Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 37(16Q23.1) MUTATED	96	27	19
DEL PEAK 37(16Q23.1) WILD-TYPE	69	62	152

Figure S644. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S645. Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 37(16Q23.1) MUTATED	16	133	17
DEL PEAK 37(16Q23.1) WILD-TYPE	135	97	132

Figure S645. 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 = 0.012

Table S646. Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 37(16Q23.1) MUTATED	38	112	16
DEL PEAK 37(16Q23.1) WILD-TYPE	178	57	129

Figure S646. 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 = 0.012

Table S647. Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 37(16Q23.1) MUTATED	120	23	18
DEL PEAK 37(16Q23.1) WILD-TYPE	106	120	143

Figure S647. 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 = 0.012

Table S648. Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 37(16Q23.1) MUTATED	16	7	92	46
DEL PEAK 37(16Q23.1) WILD-TYPE	125	53	31	160

Figure S648. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S649. Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 37(16Q23.1) MUTATED	80	35	23
DEL PEAK 37(16Q23.1) WILD-TYPE	92	61	107

Figure S649. 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 = 0.012

Table S650. Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 37(16Q23.1) MUTATED	72	15	51
DEL PEAK 37(16Q23.1) WILD-TYPE	72	100	88

Figure S650. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S651. 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 38(17P13.3) MUTATED	1	7	1	0	0
DEL PEAK 38(17P13.3) WILD-TYPE	13	2	6	7	16

Figure S651. 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 = 0.012

Table S652. Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 38(17P13.3) MUTATED	109	4	5	1	3
DEL PEAK 38(17P13.3) WILD-TYPE	60	301	14	8	34

Figure S652. 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 = 0.012

Table S653. Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 38(17P13.3) MUTATED	71	20	13
DEL PEAK 38(17P13.3) WILD-TYPE	94	69	158

Figure S653. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S654. Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 38(17P13.3) MUTATED	6	98	15
DEL PEAK 38(17P13.3) WILD-TYPE	145	132	134

Figure S654. 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 = 0.012

Table S655. Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 38(17P13.3) MUTATED	19	84	16
DEL PEAK 38(17P13.3) WILD-TYPE	197	85	129

Figure S655. 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 = 0.012

Table S656. Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 38(17P13.3) MUTATED	91	13	15
DEL PEAK 38(17P13.3) WILD-TYPE	135	130	146

Figure S656. 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 = 0.012

Table S657. Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 38(17P13.3) MUTATED	15	2	65	37
DEL PEAK 38(17P13.3) WILD-TYPE	126	58	58	169

Figure S657. 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 = 0.012

Table S658. Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 38(17P13.3) MUTATED	60	26	14
DEL PEAK 38(17P13.3) WILD-TYPE	112	70	116

Figure S658. 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 = 5e-05 (Fisher's exact test), Q value = 0.026

Table S659. Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 38(17P13.3) MUTATED	53	15	32
DEL PEAK 38(17P13.3) WILD-TYPE	91	100	107

Figure S659. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S660. 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 39(17P11.2) MUTATED	0	8	1	0	0
DEL PEAK 39(17P11.2) WILD-TYPE	14	1	6	7	16

Figure S660. 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 = 0.012

Table S661. Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 39(17P11.2) MUTATED	116	4	4	1	3
DEL PEAK 39(17P11.2) WILD-TYPE	53	301	15	8	34

Figure S661. 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 = 0.012

Table S662. Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 39(17P11.2) MUTATED	79	21	12
DEL PEAK 39(17P11.2) WILD-TYPE	86	68	159

Figure S662. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S663. Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 39(17P11.2) MUTATED	4	108	14
DEL PEAK 39(17P11.2) WILD-TYPE	147	122	135

Figure S663. 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 = 0.012

Table S664. Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 39(17P11.2) MUTATED	18	93	15
DEL PEAK 39(17P11.2) WILD-TYPE	198	76	130

Figure S664. 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 = 0.012

Table S665. Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 39(17P11.2) MUTATED	97	11	16
DEL PEAK 39(17P11.2) WILD-TYPE	129	132	145

Figure S665. 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 = 0.012

Table S666. Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 39(17P11.2) MUTATED	15	1	72	36
DEL PEAK 39(17P11.2) WILD-TYPE	126	59	51	170

Figure S666. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S667. Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 39(17P11.2) MUTATED	63	29	15
DEL PEAK 39(17P11.2) WILD-TYPE	109	67	115

Figure S667. 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 = 1e-05 (Fisher's exact test), Q value = 0.012

Table S668. Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 39(17P11.2) MUTATED	57	15	35
DEL PEAK 39(17P11.2) WILD-TYPE	87	100	104

Figure S668. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S669. 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 40(17Q11.2) MUTATED	0	7	0	0	0
DEL PEAK 40(17Q11.2) WILD-TYPE	14	2	7	7	16

Figure S669. 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 = 0.012

Table S670. Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 40(17Q11.2) MUTATED	93	2	5	1	4
DEL PEAK 40(17Q11.2) WILD-TYPE	76	303	14	8	33

Figure S670. 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 = 0.012

Table S671. Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 40(17Q11.2) MUTATED	58	18	14
DEL PEAK 40(17Q11.2) WILD-TYPE	107	71	157

Figure S671. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S672. Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 40(17Q11.2) MUTATED	6	83	14
DEL PEAK 40(17Q11.2) WILD-TYPE	145	147	135

Figure S672. 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 = 0.012

Table S673. Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 40(17Q11.2) MUTATED	22	66	15
DEL PEAK 40(17Q11.2) WILD-TYPE	194	103	130

Figure S673. 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 = 0.012

Table S674. Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 40(17Q11.2) MUTATED	75	10	16
DEL PEAK 40(17Q11.2) WILD-TYPE	151	133	145

Figure S674. 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 = 0.012

Table S675. Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 40(17Q11.2) MUTATED	15	2	50	34
DEL PEAK 40(17Q11.2) WILD-TYPE	126	58	73	172

Figure S675. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S676. Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 41(17Q21.31) MUTATED	0	9	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	14	8	12	10

Figure S676. 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 = 0.012

Table S677. 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 41(17Q21.31) MUTATED	1	8	0	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	13	1	7	7	16

Figure S677. 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 = 0.012

Table S678. Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 41(17Q21.31) MUTATED	104	1	4	1	4
DEL PEAK 41(17Q21.31) WILD-TYPE	65	304	15	8	33

Figure S678. 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 = 0.012

Table S679. Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 41(17Q21.31) MUTATED	64	22	13
DEL PEAK 41(17Q21.31) WILD-TYPE	101	67	158

Figure S679. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S680. Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 41(17Q21.31) MUTATED	5	91	15
DEL PEAK 41(17Q21.31) WILD-TYPE	146	139	134

Figure S680. 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 = 0.012

Table S681. Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 41(17Q21.31) MUTATED	20	76	15
DEL PEAK 41(17Q21.31) WILD-TYPE	196	93	130

Figure S681. 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 = 0.012

Table S682. Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 41(17Q21.31) MUTATED	80	12	17
DEL PEAK 41(17Q21.31) WILD-TYPE	146	131	144

Figure S682. 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 = 0.012

Table S683. Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 41(17Q21.31) MUTATED	17	1	58	33
DEL PEAK 41(17Q21.31) WILD-TYPE	124	59	65	173

Figure S683. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.054

Table S684. Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 41(17Q21.31) MUTATED	58	21	17
DEL PEAK 41(17Q21.31) WILD-TYPE	114	75	113

Figure S684. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S685. Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 42(18Q21.2) MUTATED	74	2	8	4	3
DEL PEAK 42(18Q21.2) WILD-TYPE	95	303	11	5	34

Figure S685. 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 = 0.012

Table S686. Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 42(18Q21.2) MUTATED	57	14	10
DEL PEAK 42(18Q21.2) WILD-TYPE	108	75	161

Figure S686. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S687. Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 42(18Q21.2) MUTATED	5	75	11
DEL PEAK 42(18Q21.2) WILD-TYPE	146	155	138

Figure S687. 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 = 0.012

Table S688. Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 42(18Q21.2) MUTATED	25	56	10
DEL PEAK 42(18Q21.2) WILD-TYPE	191	113	135

Figure S688. 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 = 0.012

Table S689. Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 42(18Q21.2) MUTATED	72	7	11
DEL PEAK 42(18Q21.2) WILD-TYPE	154	136	150

Figure S689. 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 = 0.012

Table S690. Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 42(18Q21.2) MUTATED	8	1	48	33
DEL PEAK 42(18Q21.2) WILD-TYPE	133	59	75	173

Figure S690. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S691. Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 42(18Q21.2) MUTATED	44	10	25
DEL PEAK 42(18Q21.2) WILD-TYPE	100	105	114

Figure S691. 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 = 0.012

Table S692. Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 43(18Q23) MUTATED	80	2	9	3	4
DEL PEAK 43(18Q23) WILD-TYPE	89	303	10	6	33

Figure S692. 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 = 0.012

Table S693. Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 43(18Q23) MUTATED	62	14	10
DEL PEAK 43(18Q23) WILD-TYPE	103	75	161

Figure S693. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S694. Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 43(18Q23) MUTATED	5	81	11
DEL PEAK 43(18Q23) WILD-TYPE	146	149	138

Figure S694. 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 = 0.012

Table S695. Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 43(18Q23) MUTATED	23	63	11
DEL PEAK 43(18Q23) WILD-TYPE	193	106	134

Figure S695. 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 = 0.012

Table S696. Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 43(18Q23) MUTATED	75	9	12
DEL PEAK 43(18Q23) WILD-TYPE	151	134	149

Figure S696. 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 = 0.012

Table S697. Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 43(18Q23) MUTATED	10	2	54	30
DEL PEAK 43(18Q23) WILD-TYPE	131	58	69	176

Figure S697. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.12

Table S698. Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 43(18Q23) MUTATED	49	22	13
DEL PEAK 43(18Q23) WILD-TYPE	123	74	117

Figure S698. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.063

Table S699. Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 43(18Q23) MUTATED	44	11	29
DEL PEAK 43(18Q23) WILD-TYPE	100	104	110

Figure S699. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S700. Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 44(19P13.3) MUTATED	0	11	0	0
DEL PEAK 44(19P13.3) WILD-TYPE	14	6	12	10

Figure S700. 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 = 0.012

Table S701. 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 44(19P13.3) MUTATED	2	9	0	0	0
DEL PEAK 44(19P13.3) WILD-TYPE	12	0	7	7	16

Figure S701. 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 = 0.012

Table S702. Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 44(19P13.3) MUTATED	145	0	5	3	1
DEL PEAK 44(19P13.3) WILD-TYPE	24	305	14	6	36

Figure S702. 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 = 0.012

Table S703. Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 44(19P13.3) MUTATED	108	23	5
DEL PEAK 44(19P13.3) WILD-TYPE	57	66	166

Figure S703. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S704. Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
DEL PEAK 44(19P13.3) MUTATED	7	14	2	0	1	7
DEL PEAK 44(19P13.3) WILD-TYPE	34	23	37	12	40	17

Figure S704. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S705. Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 44(19P13.3) MUTATED	4	138	9
DEL PEAK 44(19P13.3) WILD-TYPE	147	92	140

Figure S705. 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 = 0.012

Table S706. Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 44(19P13.3) MUTATED	23	120	8
DEL PEAK 44(19P13.3) WILD-TYPE	193	49	137

Figure S706. 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 = 0.012

Table S707. Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 44(19P13.3) MUTATED	130	9	10
DEL PEAK 44(19P13.3) WILD-TYPE	96	134	151

Figure S707. 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 = 0.012

Table S708. Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 44(19P13.3) MUTATED	13	1	98	37
DEL PEAK 44(19P13.3) WILD-TYPE	128	59	25	169

Figure S708. 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 = 0.012

Table S709. Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 44(19P13.3) MUTATED	83	31	18
DEL PEAK 44(19P13.3) WILD-TYPE	89	65	112

Figure S709. 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 = 0.012

Table S710. Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 44(19P13.3) MUTATED	78	11	43
DEL PEAK 44(19P13.3) WILD-TYPE	66	104	96

Figure S710. 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 = 0.012

Table S711. Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 45(19P12) MUTATED	50	1	5	1	1
DEL PEAK 45(19P12) WILD-TYPE	119	304	14	8	36

Figure S711. 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 = 0.012

Table S712. Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 45(19P12) MUTATED	38	10	4
DEL PEAK 45(19P12) WILD-TYPE	127	79	167

Figure S712. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S713. Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 45(19P12) MUTATED	5	46	6
DEL PEAK 45(19P12) WILD-TYPE	146	184	143

Figure S713. 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 = 0.012

Table S714. Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 45(19P12) MUTATED	13	39	5
DEL PEAK 45(19P12) WILD-TYPE	203	130	140

Figure S714. 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 = 0.012

Table S715. Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 45(19P12) MUTATED	44	8	5
DEL PEAK 45(19P12) WILD-TYPE	182	135	156

Figure S715. 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 = 0.012

Table S716. Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 45(19P12) MUTATED	5	2	28	22
DEL PEAK 45(19P12) WILD-TYPE	136	58	95	184

Figure S716. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S717. Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 45(19P12) MUTATED	32	5	13
DEL PEAK 45(19P12) WILD-TYPE	112	110	126

Figure S717. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.021

Table S718. 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 46(19Q13.43) MUTATED	1	7	1	0	0
DEL PEAK 46(19Q13.43) WILD-TYPE	13	2	6	7	16

Figure S718. 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 = 0.012

Table S719. Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 46(19Q13.43) MUTATED	61	1	3	1	1
DEL PEAK 46(19Q13.43) WILD-TYPE	108	304	16	8	36

Figure S719. 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 = 0.012

Table S720. Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 46(19Q13.43) MUTATED	43	11	2
DEL PEAK 46(19Q13.43) WILD-TYPE	122	78	169

Figure S720. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S721. Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 46(19Q13.43) MUTATED	3	58	4
DEL PEAK 46(19Q13.43) WILD-TYPE	148	172	145

Figure S721. 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 = 0.012

Table S722. Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 46(19Q13.43) MUTATED	11	51	3
DEL PEAK 46(19Q13.43) WILD-TYPE	205	118	142

Figure S722. 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 = 0.012

Table S723. Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 46(19Q13.43) MUTATED	55	4	4
DEL PEAK 46(19Q13.43) WILD-TYPE	171	139	157

Figure S723. 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 = 0.012

Table S724. Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 46(19Q13.43) MUTATED	3	1	39	20
DEL PEAK 46(19Q13.43) WILD-TYPE	138	59	84	186

Figure S724. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S725. Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 46(19Q13.43) MUTATED	29	2	25
DEL PEAK 46(19Q13.43) WILD-TYPE	115	113	114

Figure S725. 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 = 0.012

Table S726. Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 47(20P12.1) MUTATED	25	6	2	1	2
DEL PEAK 47(20P12.1) WILD-TYPE	144	299	17	8	35

Figure S726. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.23

Table S727. Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 47(20P12.1) MUTATED	3	26	6
DEL PEAK 47(20P12.1) WILD-TYPE	148	204	143

Figure S727. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.2

Table S728. Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 47(20P12.1) MUTATED	8	22	5
DEL PEAK 47(20P12.1) WILD-TYPE	208	147	140

Figure S728. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.24

Table S729. Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 47(20P12.1) MUTATED	26	5	4
DEL PEAK 47(20P12.1) WILD-TYPE	200	138	157

Figure S729. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.22

Table S730. Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 47(20P12.1) MUTATED	7	2	19	7
DEL PEAK 47(20P12.1) WILD-TYPE	134	58	104	199

Figure S730. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.026

Table S731. Gene #99: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 48(22Q13.32) MUTATED	0	9	0	0
DEL PEAK 48(22Q13.32) WILD-TYPE	14	8	12	10

Figure S731. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.016

Table S732. Gene #99: '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 48(22Q13.32) MUTATED	2	7	0	0	0
DEL PEAK 48(22Q13.32) WILD-TYPE	12	2	7	7	16

Figure S732. Get High-res Image Gene #99: '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 = 0.012

Table S733. Gene #99: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 48(22Q13.32) MUTATED	122	7	4	5	3
DEL PEAK 48(22Q13.32) WILD-TYPE	47	298	15	4	34

Figure S733. Get High-res Image Gene #99: '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 = 0.012

Table S734. Gene #99: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 48(22Q13.32) MUTATED	84	23	18
DEL PEAK 48(22Q13.32) WILD-TYPE	81	66	153

Figure S734. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S735. Gene #99: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 48(22Q13.32) MUTATED	8	111	19
DEL PEAK 48(22Q13.32) WILD-TYPE	143	119	130

Figure S735. Get High-res Image Gene #99: '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 = 0.012

Table S736. Gene #99: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 48(22Q13.32) MUTATED	28	91	19
DEL PEAK 48(22Q13.32) WILD-TYPE	188	78	126

Figure S736. Get High-res Image Gene #99: '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 = 0.012

Table S737. Gene #99: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 48(22Q13.32) MUTATED	105	12	20
DEL PEAK 48(22Q13.32) WILD-TYPE	121	131	141

Figure S737. Get High-res Image Gene #99: '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 = 0.012

Table S738. Gene #99: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 48(22Q13.32) MUTATED	19	1	75	42
DEL PEAK 48(22Q13.32) WILD-TYPE	122	59	48	164

Figure S738. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.035

Table S739. Gene #99: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 48(22Q13.32) MUTATED	69	28	22
DEL PEAK 48(22Q13.32) WILD-TYPE	103	68	108

Figure S739. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.012

Table S740. Gene #99: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 48(22Q13.32) MUTATED	64	19	36
DEL PEAK 48(22Q13.32) WILD-TYPE	80	96	103

Figure S740. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S741. Gene #100: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 49(XP21.1) MUTATED	78	2	3	2	3
DEL PEAK 49(XP21.1) WILD-TYPE	91	303	16	7	34

Figure S741. Get High-res Image Gene #100: '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 = 0.012

Table S742. Gene #100: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 49(XP21.1) MUTATED	54	12	9
DEL PEAK 49(XP21.1) WILD-TYPE	111	77	162

Figure S742. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S743. Gene #100: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	151	230	149
DEL PEAK 49(XP21.1) MUTATED	5	75	6
DEL PEAK 49(XP21.1) WILD-TYPE	146	155	143

Figure S743. Get High-res Image Gene #100: '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 = 0.012

Table S744. Gene #100: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	216	169	145
DEL PEAK 49(XP21.1) MUTATED	17	64	5
DEL PEAK 49(XP21.1) WILD-TYPE	199	105	140

Figure S744. Get High-res Image Gene #100: '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 = 0.012

Table S745. Gene #100: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	226	143	161
DEL PEAK 49(XP21.1) MUTATED	67	9	9
DEL PEAK 49(XP21.1) WILD-TYPE	159	134	152

Figure S745. Get High-res Image Gene #100: '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 = 0.012

Table S746. Gene #100: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	141	60	123	206
DEL PEAK 49(XP21.1) MUTATED	8	2	48	27
DEL PEAK 49(XP21.1) WILD-TYPE	133	58	75	179

Figure S746. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.072

Table S747. Gene #100: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 49(XP21.1) MUTATED	47	17	11
DEL PEAK 49(XP21.1) WILD-TYPE	125	79	119

Figure S747. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.012

Table S748. Gene #100: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 49(XP21.1) MUTATED	44	6	25
DEL PEAK 49(XP21.1) WILD-TYPE	100	109	114

Figure S748. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 539
Number of significantly focal cnvs = 100
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