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 99 focal events and 12 molecular subtypes across 524 patients, 706 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', and 'MIRSEQ_CHIERARCHICAL'.
amp_1p34.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p22.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 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', and 'MIRSEQ_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', and 'MIRSEQ_CHIERARCHICAL'.
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', and 'MIRSEQ_CHIERARCHICAL'.
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', and 'MIRSEQ_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', and 'MIRSEQ_CHIERARCHICAL'.
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_6q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_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_9p24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_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', and 'MIRSEQ_MATURE_CNMF'.
amp_12q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_12q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_14q24.3 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', and 'MIRSEQ_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', and 'MIRSEQ_MATURE_CNMF'.
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_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_19p13.12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_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', and 'MIRSEQ_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_CNMF'.
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_CNMF'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
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', '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_4p15.31 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_5q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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', and 'MIRSEQ_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', and 'MIRSEQ_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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', 'MIRSEQ_MATURE_CNMF', 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_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', and 'MIRSEQ_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_17p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
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', and 'MIRSEQ_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF'.
del_22q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 99 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, 706 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	167 (32%)	357	0.0001 (0.0536)	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	0.00016 (0.0816)	0.00858 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)
del 19p13 3	147 (28%)	377	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	3e-05 (0.0173)	0.0124 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
amp 3q26 2	156 (30%)	368	0.00033 (0.16)	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	0.00071 (0.319)	0.0161 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
amp 6p24 2	111 (21%)	413	0.00273 (1.00)	0.00072 (0.323)	1e-05 (0.0117)	1e-05 (0.0117)	0.00017 (0.0864)	0.218 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	4e-05 (0.0225)	0.00032 (0.156)
amp 8q24 21	208 (40%)	316	0.00261 (1.00)	0.00572 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00726 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0001 (0.0536)	0.00038 (0.182)
amp 17q25 1	100 (19%)	424	4e-05 (0.0225)	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	0.00524 (1.00)	0.109 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	0.00054 (0.251)
amp 19p13 2	88 (17%)	436	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.15 (1.00)	0.0016 (0.674)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00053 (0.248)	0.0154 (1.00)
amp 19q12	115 (22%)	409	0.0051 (1.00)	6e-05 (0.0333)	1e-05 (0.0117)	1e-05 (0.0117)	0.0046 (1.00)	0.00128 (0.548)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00013 (0.0676)
amp 20q11 21	142 (27%)	382	0.0026 (1.00)	0.00015 (0.0768)	1e-05 (0.0117)	1e-05 (0.0117)	0.00109 (0.474)	0.22 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00038 (0.182)
del 4q22 1	102 (19%)	422	0.00372 (1.00)	0.00013 (0.0676)	1e-05 (0.0117)	1e-05 (0.0117)	0.0141 (1.00)	0.224 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)
del 4q34 3	125 (24%)	399	0.00378 (1.00)	0.00013 (0.0676)	1e-05 (0.0117)	1e-05 (0.0117)	0.0633 (1.00)	0.573 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 5q11 2	106 (20%)	418	0.0129 (1.00)	0.00962 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00028 (0.137)	0.0136 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	6e-05 (0.0333)
del 8p23 2	113 (22%)	411	0.00191 (0.789)	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	0.0447 (1.00)	0.0168 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 8p21 2	111 (21%)	413	0.00194 (0.799)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0189 (1.00)	0.0019 (0.787)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 9q21 2	123 (23%)	401	5e-05 (0.0279)	3e-05 (0.0173)	1e-05 (0.0117)	1e-05 (0.0117)	0.00032 (0.156)	0.701 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00091 (0.4)	0.0104 (1.00)
del 9q34 2	128 (24%)	396	4e-05 (0.0225)	3e-05 (0.0173)	1e-05 (0.0117)	1e-05 (0.0117)	0.00054 (0.251)	0.339 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	0.00114 (0.495)
del 15q23	110 (21%)	414	0.00206 (0.838)	0.00046 (0.218)	1e-05 (0.0117)	1e-05 (0.0117)	0.119 (1.00)	0.742 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 16q21	150 (29%)	374	0.00082 (0.362)	8e-05 (0.0434)	1e-05 (0.0117)	1e-05 (0.0117)	0.0892 (1.00)	0.542 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 16q23 1	161 (31%)	363	0.00301 (1.00)	0.00026 (0.128)	1e-05 (0.0117)	1e-05 (0.0117)	0.0362 (1.00)	0.899 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 17p11 2	116 (22%)	408	0.00013 (0.0676)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0215 (1.00)	0.284 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00019 (0.0956)	0.00305 (1.00)
del 19q13 43	64 (12%)	460	0.00068 (0.306)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.106 (1.00)	0.191 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	6e-05 (0.0333)	9e-05 (0.0484)
del 22q13 31	132 (25%)	392	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0014 (0.595)	0.217 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00026 (0.128)	0.00229 (0.918)
amp 1p34 2	71 (14%)	453	0.0128 (1.00)	0.00096 (0.42)	1e-05 (0.0117)	1e-05 (0.0117)	0.0202 (1.00)	0.106 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	4e-05 (0.0225)	1e-05 (0.0117)
amp 2q13	114 (22%)	410	0.159 (1.00)	0.0293 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00254 (1.00)	0.034 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	6e-05 (0.0333)
amp 5p15 33	83 (16%)	441	0.23 (1.00)	0.044 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.294 (1.00)	0.445 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
amp 8q24 21	202 (39%)	322	0.0125 (1.00)	0.0743 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	7e-05 (0.0384)	0.0243 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00016 (0.0816)	0.0024 (0.953)
amp 17q11 2	67 (13%)	457	0.151 (1.00)	0.0518 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00699 (1.00)	0.068 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	0.00025 (0.123)
amp 17q12	71 (14%)	453	0.108 (1.00)	0.00215 (0.871)	1e-05 (0.0117)	1e-05 (0.0117)	0.00543 (1.00)	0.0545 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)
amp 18p11 31	91 (17%)	433	0.157 (1.00)	0.0546 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00532 (1.00)	0.088 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0002 (0.1)
amp 18q11 2	67 (13%)	457	0.108 (1.00)	0.182 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.181 (1.00)	0.0221 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
amp 19p13 12	91 (17%)	433	0.00382 (1.00)	0.0002 (0.1)	1e-05 (0.0117)	1e-05 (0.0117)	0.0335 (1.00)	0.0077 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	3e-05 (0.0173)	0.0023 (0.92)
amp 20p13	113 (22%)	411	0.152 (1.00)	0.0499 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.122 (1.00)	0.268 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	0.00011 (0.0584)
amp 20q13 12	145 (28%)	379	0.013 (1.00)	0.00989 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0052 (1.00)	0.335 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0001 (0.0536)	0.00018 (0.0909)
amp 22q12 2	59 (11%)	465	0.38 (1.00)	0.196 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.114 (1.00)	0.00436 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)
del 1p36 11	82 (16%)	442	0.0502 (1.00)	0.00751 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0226 (1.00)	0.619 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	7e-05 (0.0384)
del 3p14 2	75 (14%)	449	0.0514 (1.00)	0.00769 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00356 (1.00)	0.0738 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	7e-05 (0.0384)	0.00012 (0.0626)
del 4p16 3	91 (17%)	433	0.013 (1.00)	0.00095 (0.416)	1e-05 (0.0117)	1e-05 (0.0117)	0.00414 (1.00)	0.407 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	0.00019 (0.0956)
del 4p15 31	95 (18%)	429	0.0129 (1.00)	0.00969 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00836 (1.00)	0.498 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)
del 7p22 3	70 (13%)	454	0.00051 (0.239)	0.0101 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00639 (1.00)	0.00993 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00014 (0.0721)	0.00054 (0.251)
del 7q36 1	62 (12%)	462	0.336 (1.00)	0.079 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.011 (1.00)	0.00361 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00014 (0.0721)	0.00041 (0.195)
del 11p15 5	99 (19%)	425	0.38 (1.00)	0.195 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.287 (1.00)	0.0685 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	3e-05 (0.0173)	0.00014 (0.0721)
del 11q14 1	66 (13%)	458			1e-05 (0.0117)	1e-05 (0.0117)	0.504 (1.00)	0.585 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00021 (0.104)	0.00053 (0.248)
del 11q25	89 (17%)	435			1e-05 (0.0117)	1e-05 (0.0117)	0.111 (1.00)	1 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	0.00013 (0.0676)
del 12q23 1	53 (10%)	471			1e-05 (0.0117)	1e-05 (0.0117)	0.0379 (1.00)	0.023 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	0.00023 (0.114)
del 12q24 33	64 (12%)	460			1e-05 (0.0117)	1e-05 (0.0117)	0.0661 (1.00)	0.0951 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	1e-05 (0.0117)
del 14q13 1	69 (13%)	455	0.0082 (1.00)	0.00479 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.059 (1.00)	0.179 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	5e-05 (0.0279)	0.00035 (0.169)
del 15q15 1	135 (26%)	389	0.0121 (1.00)	0.00125 (0.539)	1e-05 (0.0117)	1e-05 (0.0117)	0.00259 (1.00)	0.291 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)
del 16p13 3	88 (17%)	436	0.0134 (1.00)	0.0101 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0639 (1.00)	0.0483 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0001 (0.0536)	3e-05 (0.0173)
del 17p11 2	122 (23%)	402	0.00067 (0.304)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00376 (1.00)	0.141 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00047 (0.221)	0.00455 (1.00)
del 17q21 31	100 (19%)	424	0.0004 (0.19)	6e-05 (0.0333)	1e-05 (0.0117)	1e-05 (0.0117)	0.0332 (1.00)	0.765 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00414 (1.00)	0.0943 (1.00)
amp 1p35 2	55 (10%)	469	0.0518 (1.00)	0.00053 (0.248)	1e-05 (0.0117)	1e-05 (0.0117)	0.00064 (0.292)	0.142 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00177 (0.735)	0.00074 (0.33)
amp 1q21 3	233 (44%)	291	0.0146 (1.00)	0.00553 (1.00)	1e-05 (0.0117)	0.00044 (0.209)	0.412 (1.00)	0.302 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	5e-05 (0.0279)	0.0448 (1.00)	0.00029 (0.142)
amp 12p12 1	87 (17%)	437	0.326 (1.00)	0.539 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.524 (1.00)	0.989 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	7e-05 (0.0384)	0.00263 (1.00)
amp 12q13 11	85 (16%)	439	0.376 (1.00)	0.205 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.564 (1.00)	0.66 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	0.00501 (1.00)
amp 12q13 2	98 (19%)	426	0.181 (1.00)	0.0874 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.335 (1.00)	0.613 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	3e-05 (0.0173)	0.0024 (0.953)
amp 13q34	56 (11%)	468	0.687 (1.00)	0.167 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.225 (1.00)	0.0271 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00012 (0.0626)	0.00172 (0.719)
del 1p36 21	70 (13%)	454	0.0235 (1.00)	0.00164 (0.687)	1e-05 (0.0117)	1e-05 (0.0117)	0.00512 (1.00)	0.271 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00011 (0.0584)	0.0006 (0.276)
del 10q23 31	73 (14%)	451	0.138 (1.00)	0.168 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0698 (1.00)	1 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00019 (0.0956)	0.00535 (1.00)
del 17p13 3	115 (22%)	409	0.00067 (0.304)	2e-05 (0.0122)	1e-05 (0.0117)	1e-05 (0.0117)	0.00154 (0.65)	0.477 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00399 (1.00)	0.0241 (1.00)
del 17q11 2	101 (19%)	423	0.00062 (0.285)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0211 (1.00)	0.821 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00363 (1.00)	0.0267 (1.00)
del 18q21 2	90 (17%)	434	0.617 (1.00)	0.252 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0434 (1.00)	0.726 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00038 (0.182)	0.00076 (0.337)
del 19p12	56 (11%)	468			1e-05 (0.0117)	1e-05 (0.0117)	0.357 (1.00)	0.455 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00222 (0.897)	0.00033 (0.16)
amp 1p22 3	92 (18%)	432	0.0197 (1.00)	0.0159 (1.00)	1e-05 (0.0117)	0.00318 (1.00)	0.895 (1.00)	0.847 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	0.00282 (1.00)	1e-05 (0.0117)
amp 1q22	247 (47%)	277	0.0216 (1.00)	0.0106 (1.00)	1e-05 (0.0117)	3e-05 (0.0173)	0.2 (1.00)	0.199 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	0.0789 (1.00)	0.00327 (1.00)
amp 2p24 3	117 (22%)	407	0.681 (1.00)	0.132 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0459 (1.00)	0.247 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00065 (0.295)	0.01 (1.00)
amp 3p25 1	77 (15%)	447	0.189 (1.00)	0.0531 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.032 (1.00)	0.3 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00338 (1.00)	0.00152 (0.643)
amp 3p14 1	61 (12%)	463	0.537 (1.00)	0.511 (1.00)	1e-05 (0.0117)	0.00052 (0.243)	0.0343 (1.00)	0.666 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	0.00015 (0.0768)	3e-05 (0.0173)	0.0318 (1.00)	0.217 (1.00)
amp 4p16 3	52 (10%)	472	0.0517 (1.00)	0.00791 (1.00)	1e-05 (0.0117)	0.00011 (0.0584)	0.0917 (1.00)	0.00127 (0.545)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00412 (1.00)	0.00915 (1.00)
amp 5q35 3	54 (10%)	470	0.137 (1.00)	0.167 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	0.122 (1.00)	0.931 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0119 (1.00)	0.021 (1.00)
amp 6q25 1	84 (16%)	440	0.284 (1.00)	1 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0884 (1.00)	0.462 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00232 (0.926)	0.0387 (1.00)
amp 9p24 2	63 (12%)	461	0.128 (1.00)	0.0879 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.00125 (0.539)	0.00854 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00145 (0.615)	0.00263 (1.00)
amp 9q34 3	37 (7%)	487	0.243 (1.00)	0.014 (1.00)	1e-05 (0.0117)	0.0001 (0.0536)	0.329 (1.00)	0.694 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	9e-05 (0.0484)	3e-05 (0.0173)	0.0278 (1.00)	0.0312 (1.00)
amp 11p11 2	49 (9%)	475	0.002 (0.818)	0.00728 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	0.0276 (1.00)	0.0786 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.028 (1.00)	0.0734 (1.00)
amp 11q13 2	71 (14%)	453	0.0021 (0.853)	0.00766 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	0.0826 (1.00)	0.188 (1.00)	1e-05 (0.0117)	7e-05 (0.0384)	7e-05 (0.0384)	7e-05 (0.0384)	0.072 (1.00)	0.0358 (1.00)
amp 11q14 1	56 (11%)	468	0.378 (1.00)	0.196 (1.00)	1e-05 (0.0117)	0.0002 (0.1)	0.454 (1.00)	0.185 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	3e-05 (0.0173)	0.00032 (0.156)	0.0608 (1.00)	0.245 (1.00)
amp 14q24 3	62 (12%)	462	0.0599 (1.00)	0.0105 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0538 (1.00)	0.268 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.148 (1.00)	0.225 (1.00)
amp 16p11 2	63 (12%)	461	0.00806 (1.00)	0.00504 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0627 (1.00)	0.0976 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00322 (1.00)	0.0451 (1.00)
amp 20q13 33	142 (27%)	382	0.0237 (1.00)	0.00593 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0793 (1.00)	0.491 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00067 (0.304)	0.00173 (0.721)
del 2q22 1	46 (9%)	478	0.0386 (1.00)	0.00074 (0.33)	1e-05 (0.0117)	2e-05 (0.0122)	0.0564 (1.00)	0.0125 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	1e-05 (0.0117)	0.0073 (1.00)	0.152 (1.00)
del 6q26	45 (9%)	479	0.38 (1.00)	0.03 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.716 (1.00)	0.131 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00115 (0.498)	0.00132 (0.562)
del 7q11 22	41 (8%)	483			1e-05 (0.0117)	2e-05 (0.0122)	0.0385 (1.00)	0.0155 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0027 (1.00)	0.0603 (1.00)
del 7q31 1	53 (10%)	471	0.136 (1.00)	0.165 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0603 (1.00)	0.0124 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00075 (0.333)	0.0176 (1.00)
del 9p23	75 (14%)	449	0.381 (1.00)	0.0294 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0165 (1.00)	0.401 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0285 (1.00)	0.128 (1.00)
del 13q11	96 (18%)	428	0.333 (1.00)	0.0394 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.19 (1.00)	0.81 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0138 (1.00)	0.0812 (1.00)
del 13q14 2	103 (20%)	421	0.62 (1.00)	0.0647 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.0775 (1.00)	0.698 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.0605 (1.00)	0.086 (1.00)
del 18q23	96 (18%)	428	0.62 (1.00)	0.251 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	0.04 (1.00)	0.872 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00091 (0.4)	0.00162 (0.68)
del 22q11 1	84 (16%)	440	0.00199 (0.816)	0.00748 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	0.37 (1.00)	0.899 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	1e-05 (0.0117)	0.206 (1.00)	0.369 (1.00)
del xp21 1	84 (16%)	440	0.00062 (0.285)	0.00121 (0.523)	1e-05 (0.0117)	1e-05 (0.0117)	0.00242 (0.956)	0.822 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00062 (0.285)	0.00194 (0.799)
amp 8p11 21	156 (30%)	368	0.01 (1.00)	0.031 (1.00)	1e-05 (0.0117)	0.00949 (1.00)	0.00099 (0.432)	0.0512 (1.00)	1e-05 (0.0117)	2e-05 (0.0122)	8e-05 (0.0434)	0.00049 (0.23)	0.016 (1.00)	0.00988 (1.00)
amp 15q26 3	37 (7%)	487			1e-05 (0.0117)	0.0102 (1.00)	0.235 (1.00)	0.308 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	1e-05 (0.0117)	0.00494 (1.00)	0.115 (1.00)
amp xp11 23	87 (17%)	437	0.356 (1.00)	0.814 (1.00)	1e-05 (0.0117)	0.00035 (0.169)	0.728 (1.00)	0.863 (1.00)	0.0002 (0.1)	2e-05 (0.0122)	0.00027 (0.133)	0.00057 (0.263)	0.0153 (1.00)	0.0711 (1.00)
del 2q37 3	51 (10%)	473			1e-05 (0.0117)	3e-05 (0.0173)	0.247 (1.00)	0.815 (1.00)	1e-05 (0.0117)	8e-05 (0.0434)	4e-05 (0.0225)	0.00201 (0.82)	0.0559 (1.00)	0.233 (1.00)
del 3q13 31	31 (6%)	493	0.38 (1.00)	0.0296 (1.00)	1e-05 (0.0117)	0.00175 (0.728)	0.0501 (1.00)	0.0075 (1.00)	1e-05 (0.0117)	1e-05 (0.0117)	2e-05 (0.0122)	6e-05 (0.0333)	0.185 (1.00)	0.299 (1.00)
amp 7q22 1	90 (17%)	434	0.677 (1.00)	0.392 (1.00)	1e-05 (0.0117)	0.00228 (0.917)	0.545 (1.00)	0.925 (1.00)	3e-05 (0.0173)	0.00018 (0.0909)	0.00046 (0.218)	0.0196 (1.00)	0.0445 (1.00)	0.0539 (1.00)
del 2p25 3	25 (5%)	499			1e-05 (0.0117)	0.00036 (0.173)	0.266 (1.00)	0.0933 (1.00)	8e-05 (0.0434)	0.00017 (0.0864)	0.00064 (0.292)	0.00232 (0.926)	0.326 (1.00)	0.593 (1.00)
amp 1q44	213 (41%)	311	0.0317 (1.00)	0.0387 (1.00)	1e-05 (0.0117)	0.028 (1.00)	0.685 (1.00)	0.161 (1.00)	0.00287 (1.00)	0.0043 (1.00)	0.00017 (0.0864)	0.0739 (1.00)	0.771 (1.00)	0.462 (1.00)
amp xq28	89 (17%)	435	0.0887 (1.00)	0.0263 (1.00)	1e-05 (0.0117)	0.0501 (1.00)	0.222 (1.00)	0.727 (1.00)	0.00129 (0.551)	0.00032 (0.156)	0.00227 (0.915)	0.11 (1.00)	0.0827 (1.00)	0.834 (1.00)
amp 10q22 2	140 (27%)	384	0.0319 (1.00)	0.113 (1.00)	1e-05 (0.0117)	0.306 (1.00)	0.31 (1.00)	0.547 (1.00)	0.0288 (1.00)	0.00762 (1.00)	0.485 (1.00)	0.0213 (1.00)	0.173 (1.00)	0.0483 (1.00)
del 20p12 1	34 (6%)	490	1 (1.00)	0.513 (1.00)	2e-05 (0.0122)	0.104 (1.00)	0.142 (1.00)	0.557 (1.00)	0.00073 (0.326)	0.0009 (0.397)	0.00621 (1.00)	0.00488 (1.00)	0.273 (1.00)	0.495 (1.00)

'amp_1p35.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.25

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	305	48	154	12	5
AMP PEAK 1(1P35.2) MUTATED	0	7	48	0	0
AMP PEAK 1(1P35.2) WILD-TYPE	305	41	106	12	5

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	158	86	166
AMP PEAK 1(1P35.2) MUTATED	34	4	6
AMP PEAK 1(1P35.2) WILD-TYPE	124	82	160

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	224	150	145
AMP PEAK 1(1P35.2) MUTATED	48	1	5
AMP PEAK 1(1P35.2) WILD-TYPE	176	149	140

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	163	213	143
AMP PEAK 1(1P35.2) MUTATED	42	6	6
AMP PEAK 1(1P35.2) WILD-TYPE	121	207	137

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	141	219	155
AMP PEAK 1(1P35.2) MUTATED	6	40	6
AMP PEAK 1(1P35.2) WILD-TYPE	135	179	149

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	55	162	116	182
AMP PEAK 1(1P35.2) MUTATED	0	36	4	12
AMP PEAK 1(1P35.2) WILD-TYPE	55	126	112	170

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

'amp_1p34.2' versus 'CN_CNMF'

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

Table S8. Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 2(1P34.2) MUTATED	0	5	66	0	0
AMP PEAK 2(1P34.2) WILD-TYPE	305	43	88	12	5

Figure S8. 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 S9. Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 2(1P34.2) MUTATED	46	10	5
AMP PEAK 2(1P34.2) WILD-TYPE	112	76	161

Figure S9. 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 S10. Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 2(1P34.2) MUTATED	63	2	5
AMP PEAK 2(1P34.2) WILD-TYPE	161	148	140

Figure S10. 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 S11. Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 2(1P34.2) MUTATED	57	7	6
AMP PEAK 2(1P34.2) WILD-TYPE	106	206	137

Figure S11. 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 S12. Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 2(1P34.2) MUTATED	5	60	4
AMP PEAK 2(1P34.2) WILD-TYPE	136	159	151

Figure S12. 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 S13. Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 2(1P34.2) MUTATED	0	53	3	13
AMP PEAK 2(1P34.2) WILD-TYPE	55	109	113	169

Figure S13. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S14. Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 2(1P34.2) MUTATED	6	41	11
AMP PEAK 2(1P34.2) WILD-TYPE	115	136	83

Figure S14. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 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	171	108	113
AMP PEAK 2(1P34.2) MUTATED	42	5	11
AMP PEAK 2(1P34.2) WILD-TYPE	129	103	102

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	305	48	154	12	5
AMP PEAK 3(1P22.3) MUTATED	31	7	48	1	5
AMP PEAK 3(1P22.3) WILD-TYPE	274	41	106	11	0

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	224	150	145
AMP PEAK 3(1P22.3) MUTATED	55	27	8
AMP PEAK 3(1P22.3) WILD-TYPE	169	123	137

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	163	213	143
AMP PEAK 3(1P22.3) MUTATED	46	36	8
AMP PEAK 3(1P22.3) WILD-TYPE	117	177	135

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 = 1e-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	141	219	155
AMP PEAK 3(1P22.3) MUTATED	33	51	7
AMP PEAK 3(1P22.3) WILD-TYPE	108	168	148

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 = 2e-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	55	162	116	182
AMP PEAK 3(1P22.3) MUTATED	7	43	6	35
AMP PEAK 3(1P22.3) WILD-TYPE	48	119	110	147

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

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S21. Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 3(1P22.3) MUTATED	52	7	12
AMP PEAK 3(1P22.3) WILD-TYPE	119	101	101

Figure S21. 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 S22. Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 4(1Q21.3) MUTATED	91	29	99	9	5
AMP PEAK 4(1Q21.3) WILD-TYPE	214	19	55	3	0

Figure S22. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.21

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 4(1Q21.3) MUTATED	87	30	59
AMP PEAK 4(1Q21.3) WILD-TYPE	71	56	107

Figure S23. 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 S24. Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 4(1Q21.3) MUTATED	123	67	41
AMP PEAK 4(1Q21.3) WILD-TYPE	101	83	104

Figure S24. 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 S25. Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 4(1Q21.3) MUTATED	99	93	39
AMP PEAK 4(1Q21.3) WILD-TYPE	64	120	104

Figure S25. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

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

Table S26. Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 4(1Q21.3) MUTATED	73	114	43
AMP PEAK 4(1Q21.3) WILD-TYPE	68	105	112

Figure S26. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S27. Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 4(1Q21.3) MUTATED	23	96	35	76
AMP PEAK 4(1Q21.3) WILD-TYPE	32	66	81	106

Figure S27. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.14

Table S28. Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 4(1Q21.3) MUTATED	95	34	46
AMP PEAK 4(1Q21.3) WILD-TYPE	76	74	67

Figure S28. 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 S29. Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 5(1Q22) MUTATED	94	30	109	9	5
AMP PEAK 5(1Q22) WILD-TYPE	211	18	45	3	0

Figure S29. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S30. Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 5(1Q22) MUTATED	96	32	60
AMP PEAK 5(1Q22) WILD-TYPE	62	54	106

Figure S30. 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 S31. Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 5(1Q22) MUTATED	132	68	45
AMP PEAK 5(1Q22) WILD-TYPE	92	82	100

Figure S31. 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 S32. Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 5(1Q22) MUTATED	107	95	43
AMP PEAK 5(1Q22) WILD-TYPE	56	118	100

Figure S32. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

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

Table S33. Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 5(1Q22) MUTATED	75	121	48
AMP PEAK 5(1Q22) WILD-TYPE	66	98	107

Figure S33. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S34. Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 5(1Q22) MUTATED	24	104	40	76
AMP PEAK 5(1Q22) WILD-TYPE	31	58	76	106

Figure S34. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

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

Table S35. Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 6(1Q44) MUTATED	95	27	77	9	5
AMP PEAK 6(1Q44) WILD-TYPE	210	21	77	3	0

Figure S35. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.086

Table S36. Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 6(1Q44) MUTATED	76	89	46
AMP PEAK 6(1Q44) WILD-TYPE	65	130	109

Figure S36. 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 S37. Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 7(2P24.3) MUTATED	15	29	68	3	2
AMP PEAK 7(2P24.3) WILD-TYPE	290	19	86	9	3

Figure S37. 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 S38. Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 7(2P24.3) MUTATED	62	11	19
AMP PEAK 7(2P24.3) WILD-TYPE	96	75	147

Figure S38. 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 S39. Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 7(2P24.3) MUTATED	80	21	15
AMP PEAK 7(2P24.3) WILD-TYPE	144	129	130

Figure S39. 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 S40. Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 7(2P24.3) MUTATED	69	31	16
AMP PEAK 7(2P24.3) WILD-TYPE	94	182	127

Figure S40. 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 S41. Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 7(2P24.3) MUTATED	19	76	20
AMP PEAK 7(2P24.3) WILD-TYPE	122	143	135

Figure S41. 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 S42. Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 7(2P24.3) MUTATED	8	63	16	28
AMP PEAK 7(2P24.3) WILD-TYPE	47	99	100	154

Figure S42. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q13' versus 'CN_CNMF'

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

Table S43. Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 8(2Q13) MUTATED	7	23	82	1	1
AMP PEAK 8(2Q13) WILD-TYPE	298	25	72	11	4

Figure S43. 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 S44. Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 8(2Q13) MUTATED	67	14	10
AMP PEAK 8(2Q13) WILD-TYPE	91	72	156

Figure S44. 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 S45. Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 8(2Q13) MUTATED	91	13	8
AMP PEAK 8(2Q13) WILD-TYPE	133	137	137

Figure S45. 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 S46. Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 8(2Q13) MUTATED	82	21	9
AMP PEAK 8(2Q13) WILD-TYPE	81	192	134

Figure S46. 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 S47. Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 8(2Q13) MUTATED	14	88	10
AMP PEAK 8(2Q13) WILD-TYPE	127	131	145

Figure S47. 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 S48. Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 8(2Q13) MUTATED	5	80	10	17
AMP PEAK 8(2Q13) WILD-TYPE	50	82	106	165

Figure S48. 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 S49. Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 8(2Q13) MUTATED	8	57	24
AMP PEAK 8(2Q13) WILD-TYPE	113	120	70

Figure S49. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S50. Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 8(2Q13) MUTATED	47	9	33
AMP PEAK 8(2Q13) WILD-TYPE	124	99	80

Figure S50. 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 S51. Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 9(3P25.1) MUTATED	4	6	56	9	2
AMP PEAK 9(3P25.1) WILD-TYPE	301	42	98	3	3

Figure S51. 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 S52. Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 9(3P25.1) MUTATED	40	14	9
AMP PEAK 9(3P25.1) WILD-TYPE	118	72	157

Figure S52. 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 S53. Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 9(3P25.1) MUTATED	62	4	10
AMP PEAK 9(3P25.1) WILD-TYPE	162	146	135

Figure S53. 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 S54. Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 9(3P25.1) MUTATED	51	16	9
AMP PEAK 9(3P25.1) WILD-TYPE	112	197	134

Figure S54. 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 S55. Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 9(3P25.1) MUTATED	9	55	11
AMP PEAK 9(3P25.1) WILD-TYPE	132	164	144

Figure S55. 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 S56. Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 9(3P25.1) MUTATED	0	46	9	20
AMP PEAK 9(3P25.1) WILD-TYPE	55	116	107	162

Figure S56. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'CN_CNMF'

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

Table S57. Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 10(3P14.1) MUTATED	4	6	40	9	2
AMP PEAK 10(3P14.1) WILD-TYPE	301	42	114	3	3

Figure S57. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p14.1' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.24

Table S58. Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 10(3P14.1) MUTATED	32	10	10
AMP PEAK 10(3P14.1) WILD-TYPE	126	76	156

Figure S58. 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 S59. Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 10(3P14.1) MUTATED	46	3	11
AMP PEAK 10(3P14.1) WILD-TYPE	178	147	134

Figure S59. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S60. Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 10(3P14.1) MUTATED	36	15	9
AMP PEAK 10(3P14.1) WILD-TYPE	127	198	134

Figure S60. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.077

Table S61. Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 10(3P14.1) MUTATED	8	41	11
AMP PEAK 10(3P14.1) WILD-TYPE	133	178	144

Figure S61. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 10(3P14.1) MUTATED	0	34	9	17
AMP PEAK 10(3P14.1) WILD-TYPE	55	128	107	165

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

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S63. 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 S63. 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 S64. 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 S64. 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 S65. Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 11(3Q26.2) MUTATED	12	12	128	11	4
AMP PEAK 11(3Q26.2) WILD-TYPE	293	36	26	1	1

Figure S65. 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 S66. Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 11(3Q26.2) MUTATED	95	25	22
AMP PEAK 11(3Q26.2) WILD-TYPE	63	61	144

Figure S66. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.082

Table S67. 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 S67. 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 S68. Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 11(3Q26.2) MUTATED	134	9	22
AMP PEAK 11(3Q26.2) WILD-TYPE	90	141	123

Figure S68. 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 S69. Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 11(3Q26.2) MUTATED	115	28	22
AMP PEAK 11(3Q26.2) WILD-TYPE	48	185	121

Figure S69. 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 S70. Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 11(3Q26.2) MUTATED	14	128	21
AMP PEAK 11(3Q26.2) WILD-TYPE	127	91	134

Figure S70. 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 S71. Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 11(3Q26.2) MUTATED	1	104	18	40
AMP PEAK 11(3Q26.2) WILD-TYPE	54	58	98	142

Figure S71. 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 S72. Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 11(3Q26.2) MUTATED	22	85	32
AMP PEAK 11(3Q26.2) WILD-TYPE	99	92	62

Figure S72. 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 = 2e-05 (Fisher's exact test), Q value = 0.012

Table S73. Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 11(3Q26.2) MUTATED	81	21	37
AMP PEAK 11(3Q26.2) WILD-TYPE	90	87	76

Figure S73. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.16

Table S74. 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 S74. Get High-res Image Gene #12: '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 S75. 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 S75. 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 S76. Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 12(3Q26.2) MUTATED	8	11	122	11	4
AMP PEAK 12(3Q26.2) WILD-TYPE	297	37	32	1	1

Figure S76. 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 S77. Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 12(3Q26.2) MUTATED	94	20	19
AMP PEAK 12(3Q26.2) WILD-TYPE	64	66	147

Figure S77. 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 S78. Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 12(3Q26.2) MUTATED	127	9	18
AMP PEAK 12(3Q26.2) WILD-TYPE	97	141	127

Figure S78. 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 S79. Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 12(3Q26.2) MUTATED	110	26	18
AMP PEAK 12(3Q26.2) WILD-TYPE	53	187	125

Figure S79. 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 S80. Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 12(3Q26.2) MUTATED	14	120	18
AMP PEAK 12(3Q26.2) WILD-TYPE	127	99	137

Figure S80. 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 S81. Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 12(3Q26.2) MUTATED	1	100	14	37
AMP PEAK 12(3Q26.2) WILD-TYPE	54	62	102	145

Figure S81. 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 S82. Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 12(3Q26.2) MUTATED	18	83	28
AMP PEAK 12(3Q26.2) WILD-TYPE	103	94	66

Figure S82. 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 S83. Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 12(3Q26.2) MUTATED	77	17	35
AMP PEAK 12(3Q26.2) WILD-TYPE	94	91	78

Figure S83. 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 S84. Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 13(4P16.3) MUTATED	2	1	49	0	0
AMP PEAK 13(4P16.3) WILD-TYPE	303	47	105	12	5

Figure S84. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S85. Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 13(4P16.3) MUTATED	29	8	6
AMP PEAK 13(4P16.3) WILD-TYPE	129	78	160

Figure S85. 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 S86. Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 13(4P16.3) MUTATED	48	1	2
AMP PEAK 13(4P16.3) WILD-TYPE	176	149	143

Figure S86. 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 S87. Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 13(4P16.3) MUTATED	41	7	3
AMP PEAK 13(4P16.3) WILD-TYPE	122	206	140

Figure S87. 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 S88. Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 13(4P16.3) MUTATED	3	43	4
AMP PEAK 13(4P16.3) WILD-TYPE	138	176	151

Figure S88. 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 S89. Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 13(4P16.3) MUTATED	0	37	5	8
AMP PEAK 13(4P16.3) WILD-TYPE	55	125	111	174

Figure S89. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

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

Table S90. Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 14(5P15.33) MUTATED	4	5	73	0	1
AMP PEAK 14(5P15.33) WILD-TYPE	301	43	81	12	4

Figure S90. 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 S91. Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 14(5P15.33) MUTATED	52	11	7
AMP PEAK 14(5P15.33) WILD-TYPE	106	75	159

Figure S91. 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 S92. Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 14(5P15.33) MUTATED	73	6	3
AMP PEAK 14(5P15.33) WILD-TYPE	151	144	142

Figure S92. 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 S93. Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 14(5P15.33) MUTATED	61	16	5
AMP PEAK 14(5P15.33) WILD-TYPE	102	197	138

Figure S93. 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 S94. Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 14(5P15.33) MUTATED	10	67	5
AMP PEAK 14(5P15.33) WILD-TYPE	131	152	150

Figure S94. 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 S95. Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 14(5P15.33) MUTATED	3	59	3	17
AMP PEAK 14(5P15.33) WILD-TYPE	52	103	113	165

Figure S95. 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 S96. Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 14(5P15.33) MUTATED	6	50	13
AMP PEAK 14(5P15.33) WILD-TYPE	115	127	81

Figure S96. 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 S97. Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 14(5P15.33) MUTATED	46	5	18
AMP PEAK 14(5P15.33) WILD-TYPE	125	103	95

Figure S97. 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 S98. Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 15(5Q35.3) MUTATED	2	5	46	0	1
AMP PEAK 15(5Q35.3) WILD-TYPE	303	43	108	12	4

Figure S98. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

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

Table S99. Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 15(5Q35.3) MUTATED	32	9	6
AMP PEAK 15(5Q35.3) WILD-TYPE	126	77	160

Figure S99. 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 S100. Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 15(5Q35.3) MUTATED	47	4	3
AMP PEAK 15(5Q35.3) WILD-TYPE	177	146	142

Figure S100. 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 S101. Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 15(5Q35.3) MUTATED	40	11	3
AMP PEAK 15(5Q35.3) WILD-TYPE	123	202	140

Figure S101. 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 S102. Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 15(5Q35.3) MUTATED	7	42	4
AMP PEAK 15(5Q35.3) WILD-TYPE	134	177	151

Figure S102. 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 S103. Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 15(5Q35.3) MUTATED	3	37	3	10
AMP PEAK 15(5Q35.3) WILD-TYPE	52	125	113	172

Figure S103. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'CN_CNMF'

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

Table S104. Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 16(6P24.2) MUTATED	9	5	89	7	1
AMP PEAK 16(6P24.2) WILD-TYPE	296	43	65	5	4

Figure S104. 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 S105. Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 16(6P24.2) MUTATED	68	15	11
AMP PEAK 16(6P24.2) WILD-TYPE	90	71	155

Figure S105. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p24.2' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.086

Table S106. 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 S106. 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 S107. Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 16(6P24.2) MUTATED	91	5	15
AMP PEAK 16(6P24.2) WILD-TYPE	133	145	130

Figure S107. 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 S108. Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 16(6P24.2) MUTATED	74	23	14
AMP PEAK 16(6P24.2) WILD-TYPE	89	190	129

Figure S108. 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 S109. Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 16(6P24.2) MUTATED	13	83	12
AMP PEAK 16(6P24.2) WILD-TYPE	128	136	143

Figure S109. 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 S110. Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 16(6P24.2) MUTATED	1	71	11	25
AMP PEAK 16(6P24.2) WILD-TYPE	54	91	105	157

Figure S110. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S111. Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 16(6P24.2) MUTATED	13	57	22
AMP PEAK 16(6P24.2) WILD-TYPE	108	120	72

Figure S111. 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 = 0.00032 (Fisher's exact test), Q value = 0.16

Table S112. Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 16(6P24.2) MUTATED	54	12	26
AMP PEAK 16(6P24.2) WILD-TYPE	117	96	87

Figure S112. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

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

Table S113. Gene #17: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 17(6Q25.1) MUTATED	7	8	61	7	1
AMP PEAK 17(6Q25.1) WILD-TYPE	298	40	93	5	4

Figure S113. Get High-res Image Gene #17: '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 S114. Gene #17: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 17(6Q25.1) MUTATED	52	10	13
AMP PEAK 17(6Q25.1) WILD-TYPE	106	76	153

Figure S114. Get High-res Image Gene #17: '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 S115. Gene #17: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 17(6Q25.1) MUTATED	59	7	17
AMP PEAK 17(6Q25.1) WILD-TYPE	165	143	128

Figure S115. Get High-res Image Gene #17: '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 S116. Gene #17: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 17(6Q25.1) MUTATED	45	21	17
AMP PEAK 17(6Q25.1) WILD-TYPE	118	192	126

Figure S116. Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

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

Table S117. Gene #17: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 17(6Q25.1) MUTATED	16	56	12
AMP PEAK 17(6Q25.1) WILD-TYPE	125	163	143

Figure S117. Get High-res Image Gene #17: '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 S118. Gene #17: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 17(6Q25.1) MUTATED	2	48	11	23
AMP PEAK 17(6Q25.1) WILD-TYPE	53	114	105	159

Figure S118. Get High-res Image Gene #17: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

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

Table S119. Gene #18: 'amp_7q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 18(7Q22.1) MUTATED	13	26	45	4	2
AMP PEAK 18(7Q22.1) WILD-TYPE	292	22	109	8	3

Figure S119. Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S120. Gene #18: 'amp_7q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 18(7Q22.1) MUTATED	58	16	14
AMP PEAK 18(7Q22.1) WILD-TYPE	166	134	131

Figure S120. Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.091

Table S121. Gene #18: 'amp_7q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 18(7Q22.1) MUTATED	44	29	15
AMP PEAK 18(7Q22.1) WILD-TYPE	119	184	128

Figure S121. Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S122. Gene #18: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 18(7Q22.1) MUTATED	21	53	14
AMP PEAK 18(7Q22.1) WILD-TYPE	120	166	141

Figure S122. Get High-res Image Gene #18: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'CN_CNMF'

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

Table S123. Gene #19: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 19(8P11.21) MUTATED	39	25	78	12	2
AMP PEAK 19(8P11.21) WILD-TYPE	266	23	76	0	3

Figure S123. Get High-res Image Gene #19: '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 S124. Gene #19: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 19(8P11.21) MUTATED	94	29	33
AMP PEAK 19(8P11.21) WILD-TYPE	130	121	112

Figure S124. Get High-res Image Gene #19: '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 S125. Gene #19: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 19(8P11.21) MUTATED	73	51	32
AMP PEAK 19(8P11.21) WILD-TYPE	90	162	111

Figure S125. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.043

Table S126. Gene #19: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 19(8P11.21) MUTATED	34	87	32
AMP PEAK 19(8P11.21) WILD-TYPE	107	132	123

Figure S126. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.23

Table S127. Gene #19: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 19(8P11.21) MUTATED	8	66	28	51
AMP PEAK 19(8P11.21) WILD-TYPE	47	96	88	131

Figure S127. Get High-res Image Gene #19: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S128. Gene #20: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 20(8Q24.21) MUTATED	46	27	114	12	3
AMP PEAK 20(8Q24.21) WILD-TYPE	259	21	40	0	2

Figure S128. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

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

Table S129. Gene #20: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 20(8Q24.21) MUTATED	95	32	47
AMP PEAK 20(8Q24.21) WILD-TYPE	63	54	119

Figure S129. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S130. Gene #20: '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 20(8Q24.21) MUTATED	12	14	8	2	2	14
AMP PEAK 20(8Q24.21) WILD-TYPE	29	23	31	10	39	10

Figure S130. Get High-res Image Gene #20: '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 S131. Gene #20: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 20(8Q24.21) MUTATED	133	30	38
AMP PEAK 20(8Q24.21) WILD-TYPE	91	120	107

Figure S131. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S132. Gene #20: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 20(8Q24.21) MUTATED	107	55	39
AMP PEAK 20(8Q24.21) WILD-TYPE	56	158	104

Figure S132. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

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

Table S133. Gene #20: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 20(8Q24.21) MUTATED	35	127	37
AMP PEAK 20(8Q24.21) WILD-TYPE	106	92	118

Figure S133. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S134. Gene #20: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 20(8Q24.21) MUTATED	8	101	31	59
AMP PEAK 20(8Q24.21) WILD-TYPE	47	61	85	123

Figure S134. Get High-res Image Gene #20: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.082

Table S135. Gene #20: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 20(8Q24.21) MUTATED	34	93	40
AMP PEAK 20(8Q24.21) WILD-TYPE	87	84	54

Figure S135. Get High-res Image Gene #20: 'amp_8q24.21' 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 S136. Gene #21: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 21(8Q24.21) MUTATED	49	28	116	12	3
AMP PEAK 21(8Q24.21) WILD-TYPE	256	20	38	0	2

Figure S136. Get High-res Image Gene #21: '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 S137. Gene #21: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 21(8Q24.21) MUTATED	95	31	52
AMP PEAK 21(8Q24.21) WILD-TYPE	63	55	114

Figure S137. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

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

Table S138. Gene #21: '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 21(8Q24.21) MUTATED	12	17	7	2	2	16
AMP PEAK 21(8Q24.21) WILD-TYPE	29	20	32	10	39	8

Figure S138. Get High-res Image Gene #21: '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 S139. Gene #21: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 21(8Q24.21) MUTATED	135	33	39
AMP PEAK 21(8Q24.21) WILD-TYPE	89	117	106

Figure S139. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S140. Gene #21: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 21(8Q24.21) MUTATED	110	57	40
AMP PEAK 21(8Q24.21) WILD-TYPE	53	156	103

Figure S140. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

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

Table S141. Gene #21: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 21(8Q24.21) MUTATED	35	132	37
AMP PEAK 21(8Q24.21) WILD-TYPE	106	87	118

Figure S141. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S142. Gene #21: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 21(8Q24.21) MUTATED	9	102	33	60
AMP PEAK 21(8Q24.21) WILD-TYPE	46	60	83	122

Figure S142. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S143. Gene #21: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 21(8Q24.21) MUTATED	37	97	38
AMP PEAK 21(8Q24.21) WILD-TYPE	84	80	56

Figure S143. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.18

Table S144. Gene #21: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 21(8Q24.21) MUTATED	94	35	43
AMP PEAK 21(8Q24.21) WILD-TYPE	77	73	70

Figure S144. Get High-res Image Gene #21: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.2' versus 'CN_CNMF'

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

Table S145. Gene #22: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 22(9P24.2) MUTATED	5	3	55	0	0
AMP PEAK 22(9P24.2) WILD-TYPE	300	45	99	12	5

Figure S145. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p24.2' versus 'METHLYATION_CNMF'

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

Table S146. Gene #22: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 22(9P24.2) MUTATED	40	7	5
AMP PEAK 22(9P24.2) WILD-TYPE	118	79	161

Figure S146. Get High-res Image Gene #22: '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 S147. Gene #22: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 22(9P24.2) MUTATED	55	3	5
AMP PEAK 22(9P24.2) WILD-TYPE	169	147	140

Figure S147. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S148. Gene #22: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 22(9P24.2) MUTATED	44	14	5
AMP PEAK 22(9P24.2) WILD-TYPE	119	199	138

Figure S148. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_CNMF'

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

Table S149. Gene #22: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 22(9P24.2) MUTATED	7	53	2
AMP PEAK 22(9P24.2) WILD-TYPE	134	166	153

Figure S149. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p24.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S150. Gene #22: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 22(9P24.2) MUTATED	2	45	1	14
AMP PEAK 22(9P24.2) WILD-TYPE	53	117	115	168

Figure S150. Get High-res Image Gene #22: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

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

Table S151. Gene #23: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 23(9Q34.3) MUTATED	3	1	33	0	0
AMP PEAK 23(9Q34.3) WILD-TYPE	302	47	121	12	5

Figure S151. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S152. Gene #23: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 23(9Q34.3) MUTATED	20	6	2
AMP PEAK 23(9Q34.3) WILD-TYPE	138	80	164

Figure S152. Get High-res Image Gene #23: '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 S153. Gene #23: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 23(9Q34.3) MUTATED	32	3	1
AMP PEAK 23(9Q34.3) WILD-TYPE	192	147	144

Figure S153. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S154. Gene #23: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 23(9Q34.3) MUTATED	30	4	2
AMP PEAK 23(9Q34.3) WILD-TYPE	133	209	141

Figure S154. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.048

Table S155. Gene #23: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 23(9Q34.3) MUTATED	4	26	3
AMP PEAK 23(9Q34.3) WILD-TYPE	137	193	152

Figure S155. Get High-res Image Gene #23: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S156. Gene #23: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 23(9Q34.3) MUTATED	1	24	2	6
AMP PEAK 23(9Q34.3) WILD-TYPE	54	138	114	176

Figure S156. Get High-res Image Gene #23: '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 S157. Gene #24: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 24(10Q22.2) MUTATED	47	25	60	6	2
AMP PEAK 24(10Q22.2) WILD-TYPE	258	23	94	6	3

Figure S157. Get High-res Image Gene #24: '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 S158. Gene #25: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 25(11P11.2) MUTATED	1	7	40	1	0
AMP PEAK 25(11P11.2) WILD-TYPE	304	41	114	11	5

Figure S158. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

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

Table S159. Gene #25: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 25(11P11.2) MUTATED	28	9	4
AMP PEAK 25(11P11.2) WILD-TYPE	130	77	162

Figure S159. Get High-res Image Gene #25: '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 S160. Gene #25: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 25(11P11.2) MUTATED	40	3	6
AMP PEAK 25(11P11.2) WILD-TYPE	184	147	139

Figure S160. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S161. Gene #25: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 25(11P11.2) MUTATED	35	8	6
AMP PEAK 25(11P11.2) WILD-TYPE	128	205	137

Figure S161. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

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

Table S162. Gene #25: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 25(11P11.2) MUTATED	3	39	6
AMP PEAK 25(11P11.2) WILD-TYPE	138	180	149

Figure S162. Get High-res Image Gene #25: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S163. Gene #25: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 25(11P11.2) MUTATED	2	32	4	10
AMP PEAK 25(11P11.2) WILD-TYPE	53	130	112	172

Figure S163. Get High-res Image Gene #25: '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 S164. Gene #26: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 26(11Q13.2) MUTATED	6	10	54	1	0
AMP PEAK 26(11Q13.2) WILD-TYPE	299	38	100	11	5

Figure S164. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

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

Table S165. Gene #26: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 26(11Q13.2) MUTATED	40	8	12
AMP PEAK 26(11Q13.2) WILD-TYPE	118	78	154

Figure S165. Get High-res Image Gene #26: '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 S166. Gene #26: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 26(11Q13.2) MUTATED	50	6	14
AMP PEAK 26(11Q13.2) WILD-TYPE	174	144	131

Figure S166. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S167. Gene #26: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 26(11Q13.2) MUTATED	38	18	14
AMP PEAK 26(11Q13.2) WILD-TYPE	125	195	129

Figure S167. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S168. Gene #26: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 26(11Q13.2) MUTATED	8	46	15
AMP PEAK 26(11Q13.2) WILD-TYPE	133	173	140

Figure S168. Get High-res Image Gene #26: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S169. Gene #26: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 26(11Q13.2) MUTATED	2	38	9	20
AMP PEAK 26(11Q13.2) WILD-TYPE	53	124	107	162

Figure S169. Get High-res Image Gene #26: '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 S170. Gene #27: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 27(11Q14.1) MUTATED	4	7	44	1	0
AMP PEAK 27(11Q14.1) WILD-TYPE	301	41	110	11	5

Figure S170. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S171. Gene #27: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 27(11Q14.1) MUTATED	31	7	9
AMP PEAK 27(11Q14.1) WILD-TYPE	127	79	157

Figure S171. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

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

Table S172. Gene #27: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 27(11Q14.1) MUTATED	41	6	8
AMP PEAK 27(11Q14.1) WILD-TYPE	183	144	137

Figure S172. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S173. Gene #27: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 27(11Q14.1) MUTATED	33	13	9
AMP PEAK 27(11Q14.1) WILD-TYPE	130	200	134

Figure S173. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S174. Gene #27: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 27(11Q14.1) MUTATED	5	39	12
AMP PEAK 27(11Q14.1) WILD-TYPE	136	180	143

Figure S174. Get High-res Image Gene #27: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S175. Gene #27: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 27(11Q14.1) MUTATED	2	32	7	15
AMP PEAK 27(11Q14.1) WILD-TYPE	53	130	109	167

Figure S175. Get High-res Image Gene #27: '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 S176. Gene #28: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 28(12P12.1) MUTATED	14	14	54	2	3
AMP PEAK 28(12P12.1) WILD-TYPE	291	34	100	10	2

Figure S176. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

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

Table S177. Gene #28: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 28(12P12.1) MUTATED	49	12	10
AMP PEAK 28(12P12.1) WILD-TYPE	109	74	156

Figure S177. Get High-res Image Gene #28: '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 S178. Gene #28: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 28(12P12.1) MUTATED	63	12	11
AMP PEAK 28(12P12.1) WILD-TYPE	161	138	134

Figure S178. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S179. Gene #28: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 28(12P12.1) MUTATED	52	22	12
AMP PEAK 28(12P12.1) WILD-TYPE	111	191	131

Figure S179. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

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

Table S180. Gene #28: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 28(12P12.1) MUTATED	14	61	12
AMP PEAK 28(12P12.1) WILD-TYPE	127	158	143

Figure S180. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S181. Gene #28: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 28(12P12.1) MUTATED	6	53	11	17
AMP PEAK 28(12P12.1) WILD-TYPE	49	109	105	165

Figure S181. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S182. Gene #28: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 28(12P12.1) MUTATED	8	45	15
AMP PEAK 28(12P12.1) WILD-TYPE	113	132	79

Figure S182. Get High-res Image Gene #28: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.11' versus 'CN_CNMF'

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

Table S183. Gene #29: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 29(12Q13.11) MUTATED	11	15	55	1	3
AMP PEAK 29(12Q13.11) WILD-TYPE	294	33	99	11	2

Figure S183. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.11' versus 'METHLYATION_CNMF'

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

Table S184. Gene #29: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 29(12Q13.11) MUTATED	47	15	7
AMP PEAK 29(12Q13.11) WILD-TYPE	111	71	159

Figure S184. Get High-res Image Gene #29: '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 S185. Gene #29: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 29(12Q13.11) MUTATED	64	9	10
AMP PEAK 29(12Q13.11) WILD-TYPE	160	141	135

Figure S185. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S186. Gene #29: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 29(12Q13.11) MUTATED	55	18	10
AMP PEAK 29(12Q13.11) WILD-TYPE	108	195	133

Figure S186. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_CNMF'

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

Table S187. Gene #29: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 29(12Q13.11) MUTATED	12	62	11
AMP PEAK 29(12Q13.11) WILD-TYPE	129	157	144

Figure S187. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S188. Gene #29: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 29(12Q13.11) MUTATED	4	53	11	17
AMP PEAK 29(12Q13.11) WILD-TYPE	51	109	105	165

Figure S188. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S189. Gene #29: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 29(12Q13.11) MUTATED	7	42	16
AMP PEAK 29(12Q13.11) WILD-TYPE	114	135	78

Figure S189. Get High-res Image Gene #29: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.2' versus 'CN_CNMF'

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

Table S190. Gene #30: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 30(12Q13.2) MUTATED	14	15	65	1	3
AMP PEAK 30(12Q13.2) WILD-TYPE	291	33	89	11	2

Figure S190. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.2' versus 'METHLYATION_CNMF'

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

Table S191. Gene #30: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 30(12Q13.2) MUTATED	53	14	13
AMP PEAK 30(12Q13.2) WILD-TYPE	105	72	153

Figure S191. Get High-res Image Gene #30: '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 S192. Gene #30: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 30(12Q13.2) MUTATED	73	9	14
AMP PEAK 30(12Q13.2) WILD-TYPE	151	141	131

Figure S192. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S193. Gene #30: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 30(12Q13.2) MUTATED	60	22	14
AMP PEAK 30(12Q13.2) WILD-TYPE	103	191	129

Figure S193. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_CNMF'

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

Table S194. Gene #30: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 30(12Q13.2) MUTATED	13	68	15
AMP PEAK 30(12Q13.2) WILD-TYPE	128	151	140

Figure S194. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S195. Gene #30: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 30(12Q13.2) MUTATED	4	59	14	19
AMP PEAK 30(12Q13.2) WILD-TYPE	51	103	102	163

Figure S195. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S196. Gene #30: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 30(12Q13.2) MUTATED	11	52	14
AMP PEAK 30(12Q13.2) WILD-TYPE	110	125	80

Figure S196. Get High-res Image Gene #30: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'CN_CNMF'

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

Table S197. Gene #31: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 31(13Q34) MUTATED	4	0	50	1	1
AMP PEAK 31(13Q34) WILD-TYPE	301	48	104	11	4

Figure S197. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

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

Table S198. Gene #31: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 31(13Q34) MUTATED	36	11	4
AMP PEAK 31(13Q34) WILD-TYPE	122	75	162

Figure S198. Get High-res Image Gene #31: '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 S199. Gene #31: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 31(13Q34) MUTATED	50	3	3
AMP PEAK 31(13Q34) WILD-TYPE	174	147	142

Figure S199. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S200. Gene #31: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 31(13Q34) MUTATED	49	5	2
AMP PEAK 31(13Q34) WILD-TYPE	114	208	141

Figure S200. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

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

Table S201. Gene #31: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 31(13Q34) MUTATED	2	50	4
AMP PEAK 31(13Q34) WILD-TYPE	139	169	151

Figure S201. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202. Gene #31: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 31(13Q34) MUTATED	0	45	5	6
AMP PEAK 31(13Q34) WILD-TYPE	55	117	111	176

Figure S202. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.063

Table S203. Gene #31: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 31(13Q34) MUTATED	4	33	13
AMP PEAK 31(13Q34) WILD-TYPE	117	144	81

Figure S203. Get High-res Image Gene #31: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q24.3' versus 'CN_CNMF'

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

Table S204. Gene #32: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 32(14Q24.3) MUTATED	4	7	49	2	0
AMP PEAK 32(14Q24.3) WILD-TYPE	301	41	105	10	5

Figure S204. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q24.3' versus 'METHLYATION_CNMF'

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

Table S205. Gene #32: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 32(14Q24.3) MUTATED	36	8	8
AMP PEAK 32(14Q24.3) WILD-TYPE	122	78	158

Figure S205. Get High-res Image Gene #32: '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 S206. Gene #32: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 32(14Q24.3) MUTATED	53	1	7
AMP PEAK 32(14Q24.3) WILD-TYPE	171	149	138

Figure S206. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S207. Gene #32: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 32(14Q24.3) MUTATED	47	7	7
AMP PEAK 32(14Q24.3) WILD-TYPE	116	206	136

Figure S207. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_CNMF'

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

Table S208. Gene #32: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 32(14Q24.3) MUTATED	6	46	8
AMP PEAK 32(14Q24.3) WILD-TYPE	135	173	147

Figure S208. Get High-res Image Gene #32: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S209. Gene #32: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 32(14Q24.3) MUTATED	0	42	9	9
AMP PEAK 32(14Q24.3) WILD-TYPE	55	120	107	173

Figure S209. Get High-res Image Gene #32: 'amp_14q24.3' 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 S210. Gene #33: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 33(15Q26.3) MUTATED	4	4	29	0	0
AMP PEAK 33(15Q26.3) WILD-TYPE	301	44	125	12	5

Figure S210. Get High-res Image Gene #33: '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 S211. Gene #33: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 33(15Q26.3) MUTATED	31	4	2
AMP PEAK 33(15Q26.3) WILD-TYPE	193	146	143

Figure S211. Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S212. Gene #33: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 33(15Q26.3) MUTATED	26	9	2
AMP PEAK 33(15Q26.3) WILD-TYPE	137	204	141

Figure S212. Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

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

Table S213. Gene #33: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 33(15Q26.3) MUTATED	5	30	2
AMP PEAK 33(15Q26.3) WILD-TYPE	136	189	153

Figure S213. Get High-res Image Gene #33: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S214. Gene #33: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 33(15Q26.3) MUTATED	3	26	1	7
AMP PEAK 33(15Q26.3) WILD-TYPE	52	136	115	175

Figure S214. Get High-res Image Gene #33: '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 S215. Gene #34: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 34(16P11.2) MUTATED	2	6	54	1	0
AMP PEAK 34(16P11.2) WILD-TYPE	303	42	100	11	5

Figure S215. Get High-res Image Gene #34: '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 S216. Gene #34: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 34(16P11.2) MUTATED	36	10	8
AMP PEAK 34(16P11.2) WILD-TYPE	122	76	158

Figure S216. Get High-res Image Gene #34: '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 S217. Gene #34: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 34(16P11.2) MUTATED	54	6	3
AMP PEAK 34(16P11.2) WILD-TYPE	170	144	142

Figure S217. Get High-res Image Gene #34: '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 S218. Gene #34: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 34(16P11.2) MUTATED	46	13	4
AMP PEAK 34(16P11.2) WILD-TYPE	117	200	139

Figure S218. Get High-res Image Gene #34: '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 S219. Gene #34: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 34(16P11.2) MUTATED	4	51	5
AMP PEAK 34(16P11.2) WILD-TYPE	137	168	150

Figure S219. Get High-res Image Gene #34: '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 S220. Gene #34: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 34(16P11.2) MUTATED	4	43	4	9
AMP PEAK 34(16P11.2) WILD-TYPE	51	119	112	173

Figure S220. Get High-res Image Gene #34: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'CN_CNMF'

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

Table S221. Gene #35: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 35(17Q11.2) MUTATED	4	1	60	1	1
AMP PEAK 35(17Q11.2) WILD-TYPE	301	47	94	11	4

Figure S221. Get High-res Image Gene #35: '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 S222. Gene #35: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 35(17Q11.2) MUTATED	50	6	3
AMP PEAK 35(17Q11.2) WILD-TYPE	108	80	163

Figure S222. Get High-res Image Gene #35: '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 S223. Gene #35: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 35(17Q11.2) MUTATED	59	3	4
AMP PEAK 35(17Q11.2) WILD-TYPE	165	147	141

Figure S223. Get High-res Image Gene #35: '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 S224. Gene #35: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 35(17Q11.2) MUTATED	55	8	3
AMP PEAK 35(17Q11.2) WILD-TYPE	108	205	140

Figure S224. Get High-res Image Gene #35: '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 S225. Gene #35: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 35(17Q11.2) MUTATED	7	55	2
AMP PEAK 35(17Q11.2) WILD-TYPE	134	164	153

Figure S225. Get High-res Image Gene #35: '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 S226. Gene #35: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 35(17Q11.2) MUTATED	1	49	3	11
AMP PEAK 35(17Q11.2) WILD-TYPE	54	113	113	171

Figure S226. Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S227. Gene #35: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 35(17Q11.2) MUTATED	4	40	12
AMP PEAK 35(17Q11.2) WILD-TYPE	117	137	82

Figure S227. Get High-res Image Gene #35: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S228. Gene #35: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 35(17Q11.2) MUTATED	34	4	18
AMP PEAK 35(17Q11.2) WILD-TYPE	137	104	95

Figure S228. Get High-res Image Gene #35: '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 S229. Gene #36: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 36(17Q12) MUTATED	6	2	61	1	1
AMP PEAK 36(17Q12) WILD-TYPE	299	46	93	11	4

Figure S229. Get High-res Image Gene #36: '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 S230. Gene #36: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 36(17Q12) MUTATED	49	8	2
AMP PEAK 36(17Q12) WILD-TYPE	109	78	164

Figure S230. Get High-res Image Gene #36: '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 S231. Gene #36: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 36(17Q12) MUTATED	66	2	3
AMP PEAK 36(17Q12) WILD-TYPE	158	148	142

Figure S231. Get High-res Image Gene #36: '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 S232. Gene #36: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 36(17Q12) MUTATED	62	7	2
AMP PEAK 36(17Q12) WILD-TYPE	101	206	141

Figure S232. Get High-res Image Gene #36: '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 S233. Gene #36: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 36(17Q12) MUTATED	4	62	3
AMP PEAK 36(17Q12) WILD-TYPE	137	157	152

Figure S233. Get High-res Image Gene #36: '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 S234. Gene #36: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 36(17Q12) MUTATED	2	58	3	6
AMP PEAK 36(17Q12) WILD-TYPE	53	104	113	176

Figure S234. Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S235. Gene #36: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 36(17Q12) MUTATED	3	36	18
AMP PEAK 36(17Q12) WILD-TYPE	118	141	76

Figure S235. Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S236. Gene #36: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 36(17Q12) MUTATED	34	2	21
AMP PEAK 36(17Q12) WILD-TYPE	137	106	92

Figure S236. Get High-res Image Gene #36: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S237. Gene #37: '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 37(17Q25.1) MUTATED	0	10	1	0
AMP PEAK 37(17Q25.1) WILD-TYPE	14	7	11	10

Figure S237. Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'MRNA_CHIERARCHICAL'

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

Table S238. Gene #37: '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 37(17Q25.1) MUTATED	2	8	1	0	0
AMP PEAK 37(17Q25.1) WILD-TYPE	12	1	6	7	16

Figure S238. Get High-res Image Gene #37: '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 S239. Gene #37: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 37(17Q25.1) MUTATED	5	6	87	1	1
AMP PEAK 37(17Q25.1) WILD-TYPE	300	42	67	11	4

Figure S239. Get High-res Image Gene #37: '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 S240. Gene #37: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 37(17Q25.1) MUTATED	59	15	6
AMP PEAK 37(17Q25.1) WILD-TYPE	99	71	160

Figure S240. Get High-res Image Gene #37: '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 S241. Gene #37: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 37(17Q25.1) MUTATED	85	6	8
AMP PEAK 37(17Q25.1) WILD-TYPE	139	144	137

Figure S241. Get High-res Image Gene #37: '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 S242. Gene #37: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 37(17Q25.1) MUTATED	79	12	8
AMP PEAK 37(17Q25.1) WILD-TYPE	84	201	135

Figure S242. Get High-res Image Gene #37: '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 S243. Gene #37: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 37(17Q25.1) MUTATED	8	80	8
AMP PEAK 37(17Q25.1) WILD-TYPE	133	139	147

Figure S243. Get High-res Image Gene #37: '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 S244. Gene #37: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 37(17Q25.1) MUTATED	3	69	5	19
AMP PEAK 37(17Q25.1) WILD-TYPE	52	93	111	163

Figure S244. Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S245. Gene #37: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 37(17Q25.1) MUTATED	9	46	21
AMP PEAK 37(17Q25.1) WILD-TYPE	112	131	73

Figure S245. Get High-res Image Gene #37: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'CN_CNMF'

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

Table S246. Gene #38: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 38(18P11.31) MUTATED	5	6	79	1	0
AMP PEAK 38(18P11.31) WILD-TYPE	300	42	75	11	5

Figure S246. Get High-res Image Gene #38: '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 S247. Gene #38: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 38(18P11.31) MUTATED	57	16	7
AMP PEAK 38(18P11.31) WILD-TYPE	101	70	159

Figure S247. Get High-res Image Gene #38: '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 S248. Gene #38: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 38(18P11.31) MUTATED	80	3	8
AMP PEAK 38(18P11.31) WILD-TYPE	144	147	137

Figure S248. Get High-res Image Gene #38: '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 S249. Gene #38: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 38(18P11.31) MUTATED	73	10	8
AMP PEAK 38(18P11.31) WILD-TYPE	90	203	135

Figure S249. Get High-res Image Gene #38: '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 S250. Gene #38: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 38(18P11.31) MUTATED	6	76	8
AMP PEAK 38(18P11.31) WILD-TYPE	135	143	147

Figure S250. Get High-res Image Gene #38: '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 S251. Gene #38: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 38(18P11.31) MUTATED	2	72	7	9
AMP PEAK 38(18P11.31) WILD-TYPE	53	90	109	173

Figure S251. Get High-res Image Gene #38: '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 S252. Gene #38: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 38(18P11.31) MUTATED	7	48	23
AMP PEAK 38(18P11.31) WILD-TYPE	114	129	71

Figure S252. Get High-res Image Gene #38: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S253. Gene #38: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 38(18P11.31) MUTATED	44	8	26
AMP PEAK 38(18P11.31) WILD-TYPE	127	100	87

Figure S253. Get High-res Image Gene #38: '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 S254. Gene #39: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 39(18Q11.2) MUTATED	3	3	60	1	0
AMP PEAK 39(18Q11.2) WILD-TYPE	302	45	94	11	5

Figure S254. Get High-res Image Gene #39: '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 S255. Gene #39: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 39(18Q11.2) MUTATED	44	12	3
AMP PEAK 39(18Q11.2) WILD-TYPE	114	74	163

Figure S255. Get High-res Image Gene #39: '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 S256. Gene #39: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 39(18Q11.2) MUTATED	61	3	3
AMP PEAK 39(18Q11.2) WILD-TYPE	163	147	142

Figure S256. Get High-res Image Gene #39: '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 S257. Gene #39: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 39(18Q11.2) MUTATED	56	8	3
AMP PEAK 39(18Q11.2) WILD-TYPE	107	205	140

Figure S257. Get High-res Image Gene #39: '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 S258. Gene #39: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 39(18Q11.2) MUTATED	6	57	3
AMP PEAK 39(18Q11.2) WILD-TYPE	135	162	152

Figure S258. Get High-res Image Gene #39: '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 S259. Gene #39: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 39(18Q11.2) MUTATED	2	54	1	9
AMP PEAK 39(18Q11.2) WILD-TYPE	53	108	115	173

Figure S259. Get High-res Image Gene #39: '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 S260. Gene #39: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 39(18Q11.2) MUTATED	1	40	15
AMP PEAK 39(18Q11.2) WILD-TYPE	120	137	79

Figure S260. Get High-res Image Gene #39: '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 S261. Gene #39: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 39(18Q11.2) MUTATED	36	1	19
AMP PEAK 39(18Q11.2) WILD-TYPE	135	107	94

Figure S261. Get High-res Image Gene #39: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

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

Table S262. Gene #40: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 40(19P13.2) MUTATED	0	9	0	0
AMP PEAK 40(19P13.2) WILD-TYPE	14	8	12	10

Figure S262. Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

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

Table S263. Gene #40: '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 40(19P13.2) MUTATED	2	7	0	0	0
AMP PEAK 40(19P13.2) WILD-TYPE	12	2	7	7	16

Figure S263. Get High-res Image Gene #40: '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 S264. Gene #40: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 40(19P13.2) MUTATED	0	2	84	2	0
AMP PEAK 40(19P13.2) WILD-TYPE	305	46	70	10	5

Figure S264. Get High-res Image Gene #40: '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 S265. Gene #40: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 40(19P13.2) MUTATED	54	16	7
AMP PEAK 40(19P13.2) WILD-TYPE	104	70	159

Figure S265. Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

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

Table S266. Gene #40: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 40(19P13.2) MUTATED	78	2	7
AMP PEAK 40(19P13.2) WILD-TYPE	146	148	138

Figure S266. Get High-res Image Gene #40: '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 S267. Gene #40: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 40(19P13.2) MUTATED	69	11	7
AMP PEAK 40(19P13.2) WILD-TYPE	94	202	136

Figure S267. Get High-res Image Gene #40: '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 S268. Gene #40: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 40(19P13.2) MUTATED	4	73	8
AMP PEAK 40(19P13.2) WILD-TYPE	137	146	147

Figure S268. Get High-res Image Gene #40: '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 S269. Gene #40: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 40(19P13.2) MUTATED	1	62	8	14
AMP PEAK 40(19P13.2) WILD-TYPE	54	100	108	168

Figure S269. Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.25

Table S270. Gene #40: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 40(19P13.2) MUTATED	10	45	18
AMP PEAK 40(19P13.2) WILD-TYPE	111	132	76

Figure S270. Get High-res Image Gene #40: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S271. Gene #41: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 41(19P13.12) MUTATED	2	6	0	0	0
AMP PEAK 41(19P13.12) WILD-TYPE	12	3	7	7	16

Figure S271. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

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

Table S272. Gene #41: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 41(19P13.12) MUTATED	0	3	85	2	1
AMP PEAK 41(19P13.12) WILD-TYPE	305	45	69	10	4

Figure S272. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

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

Table S273. Gene #41: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 41(19P13.12) MUTATED	55	15	7
AMP PEAK 41(19P13.12) WILD-TYPE	103	71	159

Figure S273. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

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

Table S274. Gene #41: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 41(19P13.12) MUTATED	81	4	5
AMP PEAK 41(19P13.12) WILD-TYPE	143	146	140

Figure S274. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S275. Gene #41: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 41(19P13.12) MUTATED	72	13	5
AMP PEAK 41(19P13.12) WILD-TYPE	91	200	138

Figure S275. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

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

Table S276. Gene #41: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 41(19P13.12) MUTATED	7	75	7
AMP PEAK 41(19P13.12) WILD-TYPE	134	144	148

Figure S276. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S277. Gene #41: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 41(19P13.12) MUTATED	2	65	6	16
AMP PEAK 41(19P13.12) WILD-TYPE	53	97	110	166

Figure S277. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S278. Gene #41: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 41(19P13.12) MUTATED	8	46	20
AMP PEAK 41(19P13.12) WILD-TYPE	113	131	74

Figure S278. Get High-res Image Gene #41: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S279. Gene #42: '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 42(19Q12) MUTATED	2	7	1	0	0
AMP PEAK 42(19Q12) WILD-TYPE	12	2	6	7	16

Figure S279. Get High-res Image Gene #42: '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 S280. Gene #42: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 42(19Q12) MUTATED	3	5	105	2	0
AMP PEAK 42(19Q12) WILD-TYPE	302	43	49	10	5

Figure S280. Get High-res Image Gene #42: '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 S281. Gene #42: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 42(19Q12) MUTATED	75	18	8
AMP PEAK 42(19Q12) WILD-TYPE	83	68	158

Figure S281. Get High-res Image Gene #42: '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 S282. Gene #42: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 42(19Q12) MUTATED	106	2	7
AMP PEAK 42(19Q12) WILD-TYPE	118	148	138

Figure S282. Get High-res Image Gene #42: '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 S283. Gene #42: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 42(19Q12) MUTATED	95	14	6
AMP PEAK 42(19Q12) WILD-TYPE	68	199	137

Figure S283. Get High-res Image Gene #42: '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 S284. Gene #42: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 42(19Q12) MUTATED	6	97	8
AMP PEAK 42(19Q12) WILD-TYPE	135	122	147

Figure S284. Get High-res Image Gene #42: '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 S285. Gene #42: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 42(19Q12) MUTATED	2	88	7	14
AMP PEAK 42(19Q12) WILD-TYPE	53	74	109	168

Figure S285. Get High-res Image Gene #42: '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 S286. Gene #42: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 42(19Q12) MUTATED	10	61	26
AMP PEAK 42(19Q12) WILD-TYPE	111	116	68

Figure S286. Get High-res Image Gene #42: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.068

Table S287. Gene #42: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 42(19Q12) MUTATED	56	12	29
AMP PEAK 42(19Q12) WILD-TYPE	115	96	84

Figure S287. Get High-res Image Gene #42: '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 S288. Gene #43: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 43(20P13) MUTATED	8	20	82	1	2
AMP PEAK 43(20P13) WILD-TYPE	297	28	72	11	3

Figure S288. Get High-res Image Gene #43: '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 S289. Gene #43: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 43(20P13) MUTATED	71	16	16
AMP PEAK 43(20P13) WILD-TYPE	87	70	150

Figure S289. Get High-res Image Gene #43: '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 S290. Gene #43: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 43(20P13) MUTATED	86	12	14
AMP PEAK 43(20P13) WILD-TYPE	138	138	131

Figure S290. Get High-res Image Gene #43: '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 S291. Gene #43: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 43(20P13) MUTATED	76	19	17
AMP PEAK 43(20P13) WILD-TYPE	87	194	126

Figure S291. Get High-res Image Gene #43: '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 S292. Gene #43: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 43(20P13) MUTATED	15	82	15
AMP PEAK 43(20P13) WILD-TYPE	126	137	140

Figure S292. Get High-res Image Gene #43: '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 S293. Gene #43: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 43(20P13) MUTATED	6	72	13	21
AMP PEAK 43(20P13) WILD-TYPE	49	90	103	161

Figure S293. Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S294. Gene #43: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 43(20P13) MUTATED	16	60	20
AMP PEAK 43(20P13) WILD-TYPE	105	117	74

Figure S294. Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S295. Gene #43: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 43(20P13) MUTATED	59	14	23
AMP PEAK 43(20P13) WILD-TYPE	112	94	90

Figure S295. Get High-res Image Gene #43: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.077

Table S296. Gene #44: '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 44(20Q11.21) MUTATED	4	6	0	0	0
AMP PEAK 44(20Q11.21) WILD-TYPE	10	3	7	7	16

Figure S296. Get High-res Image Gene #44: '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 S297. Gene #44: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 44(20Q11.21) MUTATED	7	26	106	1	2
AMP PEAK 44(20Q11.21) WILD-TYPE	298	22	48	11	3

Figure S297. Get High-res Image Gene #44: '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 S298. Gene #44: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 44(20Q11.21) MUTATED	83	20	21
AMP PEAK 44(20Q11.21) WILD-TYPE	75	66	145

Figure S298. Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

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

Table S299. Gene #44: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 44(20Q11.21) MUTATED	112	10	19
AMP PEAK 44(20Q11.21) WILD-TYPE	112	140	126

Figure S299. Get High-res Image Gene #44: '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 S300. Gene #44: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 44(20Q11.21) MUTATED	96	25	20
AMP PEAK 44(20Q11.21) WILD-TYPE	67	188	123

Figure S300. Get High-res Image Gene #44: '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 S301. Gene #44: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 44(20Q11.21) MUTATED	14	106	19
AMP PEAK 44(20Q11.21) WILD-TYPE	127	113	136

Figure S301. Get High-res Image Gene #44: '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 S302. Gene #44: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 44(20Q11.21) MUTATED	6	90	17	26
AMP PEAK 44(20Q11.21) WILD-TYPE	49	72	99	156

Figure S302. Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S303. Gene #44: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 44(20Q11.21) MUTATED	22	75	22
AMP PEAK 44(20Q11.21) WILD-TYPE	99	102	72

Figure S303. Get High-res Image Gene #44: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.18

Table S304. Gene #44: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 44(20Q11.21) MUTATED	70	22	27
AMP PEAK 44(20Q11.21) WILD-TYPE	101	86	86

Figure S304. Get High-res Image Gene #44: '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 S305. Gene #45: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 45(20Q13.12) MUTATED	9	28	105	1	2
AMP PEAK 45(20Q13.12) WILD-TYPE	296	20	49	11	3

Figure S305. Get High-res Image Gene #45: '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 S306. Gene #45: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 45(20Q13.12) MUTATED	87	20	24
AMP PEAK 45(20Q13.12) WILD-TYPE	71	66	142

Figure S306. Get High-res Image Gene #45: '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 S307. Gene #45: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 45(20Q13.12) MUTATED	112	12	20
AMP PEAK 45(20Q13.12) WILD-TYPE	112	138	125

Figure S307. Get High-res Image Gene #45: '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 S308. Gene #45: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 45(20Q13.12) MUTATED	96	27	21
AMP PEAK 45(20Q13.12) WILD-TYPE	67	186	122

Figure S308. Get High-res Image Gene #45: '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 S309. Gene #45: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 45(20Q13.12) MUTATED	16	106	22
AMP PEAK 45(20Q13.12) WILD-TYPE	125	113	133

Figure S309. Get High-res Image Gene #45: '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 S310. Gene #45: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 45(20Q13.12) MUTATED	6	90	17	31
AMP PEAK 45(20Q13.12) WILD-TYPE	49	72	99	151

Figure S310. Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S311. Gene #45: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 45(20Q13.12) MUTATED	24	76	25
AMP PEAK 45(20Q13.12) WILD-TYPE	97	101	69

Figure S311. Get High-res Image Gene #45: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.091

Table S312. Gene #45: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 45(20Q13.12) MUTATED	73	22	30
AMP PEAK 45(20Q13.12) WILD-TYPE	98	86	83

Figure S312. Get High-res Image Gene #45: '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 S313. Gene #46: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 46(20Q13.33) MUTATED	10	30	99	1	2
AMP PEAK 46(20Q13.33) WILD-TYPE	295	18	55	11	3

Figure S313. Get High-res Image Gene #46: '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 S314. Gene #46: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 46(20Q13.33) MUTATED	81	21	24
AMP PEAK 46(20Q13.33) WILD-TYPE	77	65	142

Figure S314. Get High-res Image Gene #46: '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 S315. Gene #46: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 46(20Q13.33) MUTATED	107	15	20
AMP PEAK 46(20Q13.33) WILD-TYPE	117	135	125

Figure S315. Get High-res Image Gene #46: '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 S316. Gene #46: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 46(20Q13.33) MUTATED	90	30	22
AMP PEAK 46(20Q13.33) WILD-TYPE	73	183	121

Figure S316. Get High-res Image Gene #46: '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 S317. Gene #46: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 46(20Q13.33) MUTATED	16	102	22
AMP PEAK 46(20Q13.33) WILD-TYPE	125	117	133

Figure S317. Get High-res Image Gene #46: '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 S318. Gene #46: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 46(20Q13.33) MUTATED	7	87	18	28
AMP PEAK 46(20Q13.33) WILD-TYPE	48	75	98	154

Figure S318. Get High-res Image Gene #46: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

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

Table S319. Gene #47: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 47(22Q12.2) MUTATED	4	5	49	0	1
AMP PEAK 47(22Q12.2) WILD-TYPE	301	43	105	12	4

Figure S319. Get High-res Image Gene #47: '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 S320. Gene #47: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 47(22Q12.2) MUTATED	46	8	0
AMP PEAK 47(22Q12.2) WILD-TYPE	112	78	166

Figure S320. Get High-res Image Gene #47: '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 S321. Gene #47: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 47(22Q12.2) MUTATED	57	1	0
AMP PEAK 47(22Q12.2) WILD-TYPE	167	149	145

Figure S321. Get High-res Image Gene #47: '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 S322. Gene #47: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 47(22Q12.2) MUTATED	54	4	0
AMP PEAK 47(22Q12.2) WILD-TYPE	109	209	143

Figure S322. Get High-res Image Gene #47: '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 S323. Gene #47: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 47(22Q12.2) MUTATED	1	57	0
AMP PEAK 47(22Q12.2) WILD-TYPE	140	162	155

Figure S323. Get High-res Image Gene #47: '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 S324. Gene #47: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
AMP PEAK 47(22Q12.2) MUTATED	1	49	1	7
AMP PEAK 47(22Q12.2) WILD-TYPE	54	113	115	175

Figure S324. Get High-res Image Gene #47: '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 S325. Gene #47: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
AMP PEAK 47(22Q12.2) MUTATED	2	43	8
AMP PEAK 47(22Q12.2) WILD-TYPE	119	134	86

Figure S325. Get High-res Image Gene #47: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S326. Gene #47: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
AMP PEAK 47(22Q12.2) MUTATED	35	2	16
AMP PEAK 47(22Q12.2) WILD-TYPE	136	106	97

Figure S326. Get High-res Image Gene #47: '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 S327. Gene #48: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 48(XP11.23) MUTATED	11	20	44	10	2
AMP PEAK 48(XP11.23) WILD-TYPE	294	28	110	2	3

Figure S327. Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.17

Table S328. Gene #48: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
AMP PEAK 48(XP11.23) MUTATED	41	11	16
AMP PEAK 48(XP11.23) WILD-TYPE	117	75	150

Figure S328. Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.1

Table S329. Gene #48: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
AMP PEAK 48(XP11.23) MUTATED	54	15	16
AMP PEAK 48(XP11.23) WILD-TYPE	170	135	129

Figure S329. Get High-res Image Gene #48: '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 S330. Gene #48: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 48(XP11.23) MUTATED	46	23	16
AMP PEAK 48(XP11.23) WILD-TYPE	117	190	127

Figure S330. Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.13

Table S331. Gene #48: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
AMP PEAK 48(XP11.23) MUTATED	16	54	16
AMP PEAK 48(XP11.23) WILD-TYPE	125	165	139

Figure S331. Get High-res Image Gene #48: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'CN_CNMF'

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

Table S332. Gene #49: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
AMP PEAK 49(XQ28) MUTATED	13	20	45	9	2
AMP PEAK 49(XQ28) WILD-TYPE	292	28	109	3	3

Figure S332. Get High-res Image Gene #49: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S333. Gene #49: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
AMP PEAK 49(XQ28) MUTATED	44	27	16
AMP PEAK 49(XQ28) WILD-TYPE	119	186	127

Figure S333. Get High-res Image Gene #49: '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 S334. Gene #50: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 1(1P36.21) MUTATED	3	8	57	0	2
DEL PEAK 1(1P36.21) WILD-TYPE	302	40	97	12	3

Figure S334. Get High-res Image Gene #50: '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 S335. Gene #50: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 1(1P36.21) MUTATED	38	15	6
DEL PEAK 1(1P36.21) WILD-TYPE	120	71	160

Figure S335. Get High-res Image Gene #50: '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 S336. Gene #50: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 1(1P36.21) MUTATED	60	6	4
DEL PEAK 1(1P36.21) WILD-TYPE	164	144	141

Figure S336. Get High-res Image Gene #50: '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 S337. Gene #50: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 1(1P36.21) MUTATED	49	18	3
DEL PEAK 1(1P36.21) WILD-TYPE	114	195	140

Figure S337. Get High-res Image Gene #50: '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 S338. Gene #50: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 1(1P36.21) MUTATED	8	53	6
DEL PEAK 1(1P36.21) WILD-TYPE	133	166	149

Figure S338. Get High-res Image Gene #50: '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 S339. Gene #50: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 1(1P36.21) MUTATED	1	47	2	17
DEL PEAK 1(1P36.21) WILD-TYPE	54	115	114	165

Figure S339. Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S340. Gene #50: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 1(1P36.21) MUTATED	7	27	25
DEL PEAK 1(1P36.21) WILD-TYPE	114	150	69

Figure S340. Get High-res Image Gene #50: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'CN_CNMF'

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

Table S341. Gene #51: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 2(1P36.11) MUTATED	2	8	70	0	2
DEL PEAK 2(1P36.11) WILD-TYPE	303	40	84	12	3

Figure S341. Get High-res Image Gene #51: '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 S342. Gene #51: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 2(1P36.11) MUTATED	55	12	6
DEL PEAK 2(1P36.11) WILD-TYPE	103	74	160

Figure S342. Get High-res Image Gene #51: '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 S343. Gene #51: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 2(1P36.11) MUTATED	72	6	4
DEL PEAK 2(1P36.11) WILD-TYPE	152	144	141

Figure S343. Get High-res Image Gene #51: '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 S344. Gene #51: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 2(1P36.11) MUTATED	60	19	3
DEL PEAK 2(1P36.11) WILD-TYPE	103	194	140

Figure S344. Get High-res Image Gene #51: '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 S345. Gene #51: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 2(1P36.11) MUTATED	7	65	7
DEL PEAK 2(1P36.11) WILD-TYPE	134	154	148

Figure S345. Get High-res Image Gene #51: '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 S346. Gene #51: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 2(1P36.11) MUTATED	1	58	2	18
DEL PEAK 2(1P36.11) WILD-TYPE	54	104	114	164

Figure S346. Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S347. Gene #51: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 2(1P36.11) MUTATED	8	44	21
DEL PEAK 2(1P36.11) WILD-TYPE	113	133	73

Figure S347. Get High-res Image Gene #51: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S348. Gene #51: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 2(1P36.11) MUTATED	44	6	23
DEL PEAK 2(1P36.11) WILD-TYPE	127	102	90

Figure S348. Get High-res Image Gene #51: '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 S349. Gene #52: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 3(2P25.3) MUTATED	2	1	22	0	0
DEL PEAK 3(2P25.3) WILD-TYPE	303	47	132	12	5

Figure S349. Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

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

Table S350. Gene #52: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 3(2P25.3) MUTATED	18	4	2
DEL PEAK 3(2P25.3) WILD-TYPE	140	82	164

Figure S350. Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.043

Table S351. Gene #52: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 3(2P25.3) MUTATED	21	1	3
DEL PEAK 3(2P25.3) WILD-TYPE	203	149	142

Figure S351. Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.086

Table S352. Gene #52: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 3(2P25.3) MUTATED	18	4	3
DEL PEAK 3(2P25.3) WILD-TYPE	145	209	140

Figure S352. Get High-res Image Gene #52: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

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

Table S353. Gene #53: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 4(2Q22.1) MUTATED	0	4	42	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	305	44	112	12	5

Figure S353. Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

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

Table S354. Gene #53: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 4(2Q22.1) MUTATED	28	8	4
DEL PEAK 4(2Q22.1) WILD-TYPE	130	78	162

Figure S354. Get High-res Image Gene #53: '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 S355. Gene #53: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 4(2Q22.1) MUTATED	41	0	5
DEL PEAK 4(2Q22.1) WILD-TYPE	183	150	140

Figure S355. Get High-res Image Gene #53: '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 S356. Gene #53: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 4(2Q22.1) MUTATED	32	8	6
DEL PEAK 4(2Q22.1) WILD-TYPE	131	205	137

Figure S356. Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

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

Table S357. Gene #53: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 4(2Q22.1) MUTATED	4	36	4
DEL PEAK 4(2Q22.1) WILD-TYPE	137	183	151

Figure S357. Get High-res Image Gene #53: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S358. Gene #53: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 4(2Q22.1) MUTATED	0	30	4	10
DEL PEAK 4(2Q22.1) WILD-TYPE	55	132	112	172

Figure S358. Get High-res Image Gene #53: '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 S359. Gene #54: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 5(2Q37.3) MUTATED	2	7	42	0	0
DEL PEAK 5(2Q37.3) WILD-TYPE	303	41	112	12	5

Figure S359. Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S360. Gene #54: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 5(2Q37.3) MUTATED	33	6	8
DEL PEAK 5(2Q37.3) WILD-TYPE	125	80	158

Figure S360. Get High-res Image Gene #54: '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 S361. Gene #54: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 5(2Q37.3) MUTATED	40	3	7
DEL PEAK 5(2Q37.3) WILD-TYPE	184	147	138

Figure S361. Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.043

Table S362. Gene #54: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 5(2Q37.3) MUTATED	30	13	7
DEL PEAK 5(2Q37.3) WILD-TYPE	133	200	136

Figure S362. Get High-res Image Gene #54: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S363. Gene #54: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 5(2Q37.3) MUTATED	5	37	8
DEL PEAK 5(2Q37.3) WILD-TYPE	136	182	147

Figure S363. Get High-res Image Gene #54: '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 S364. Gene #55: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 6(3P14.2) MUTATED	0	8	66	0	1
DEL PEAK 6(3P14.2) WILD-TYPE	305	40	88	12	4

Figure S364. Get High-res Image Gene #55: '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 S365. Gene #55: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 6(3P14.2) MUTATED	47	12	5
DEL PEAK 6(3P14.2) WILD-TYPE	111	74	161

Figure S365. Get High-res Image Gene #55: '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 S366. Gene #55: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 6(3P14.2) MUTATED	69	1	4
DEL PEAK 6(3P14.2) WILD-TYPE	155	149	141

Figure S366. Get High-res Image Gene #55: '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 S367. Gene #55: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 6(3P14.2) MUTATED	56	13	5
DEL PEAK 6(3P14.2) WILD-TYPE	107	200	138

Figure S367. Get High-res Image Gene #55: '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 S368. Gene #55: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 6(3P14.2) MUTATED	8	61	4
DEL PEAK 6(3P14.2) WILD-TYPE	133	158	151

Figure S368. Get High-res Image Gene #55: '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 S369. Gene #55: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 6(3P14.2) MUTATED	1	53	4	15
DEL PEAK 6(3P14.2) WILD-TYPE	54	109	112	167

Figure S369. Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.038

Table S370. Gene #55: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 6(3P14.2) MUTATED	6	40	16
DEL PEAK 6(3P14.2) WILD-TYPE	115	137	78

Figure S370. Get High-res Image Gene #55: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.063

Table S371. Gene #55: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 6(3P14.2) MUTATED	39	5	18
DEL PEAK 6(3P14.2) WILD-TYPE	132	103	95

Figure S371. Get High-res Image Gene #55: '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 S372. Gene #56: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 7(3Q13.31) MUTATED	1	1	28	0	1
DEL PEAK 7(3Q13.31) WILD-TYPE	304	47	126	12	4

Figure S372. Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'MRNASEQ_CNMF'

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

Table S373. Gene #56: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 7(3Q13.31) MUTATED	27	1	3
DEL PEAK 7(3Q13.31) WILD-TYPE	197	149	142

Figure S373. Get High-res Image Gene #56: '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 S374. Gene #56: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 7(3Q13.31) MUTATED	23	5	3
DEL PEAK 7(3Q13.31) WILD-TYPE	140	208	140

Figure S374. Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

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

Table S375. Gene #56: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 7(3Q13.31) MUTATED	3	25	2
DEL PEAK 7(3Q13.31) WILD-TYPE	138	194	153

Figure S375. Get High-res Image Gene #56: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S376. Gene #56: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 7(3Q13.31) MUTATED	1	21	1	7
DEL PEAK 7(3Q13.31) WILD-TYPE	54	141	115	175

Figure S376. Get High-res Image Gene #56: '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 S377. Gene #57: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 8(4P16.3) MUTATED	4	13	71	1	2
DEL PEAK 8(4P16.3) WILD-TYPE	301	35	83	11	3

Figure S377. Get High-res Image Gene #57: '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 S378. Gene #57: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 8(4P16.3) MUTATED	59	13	7
DEL PEAK 8(4P16.3) WILD-TYPE	99	73	159

Figure S378. Get High-res Image Gene #57: '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 S379. Gene #57: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 8(4P16.3) MUTATED	76	6	9
DEL PEAK 8(4P16.3) WILD-TYPE	148	144	136

Figure S379. Get High-res Image Gene #57: '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 S380. Gene #57: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 8(4P16.3) MUTATED	66	17	8
DEL PEAK 8(4P16.3) WILD-TYPE	97	196	135

Figure S380. Get High-res Image Gene #57: '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 S381. Gene #57: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 8(4P16.3) MUTATED	8	70	10
DEL PEAK 8(4P16.3) WILD-TYPE	133	149	145

Figure S381. Get High-res Image Gene #57: '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 S382. Gene #57: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 8(4P16.3) MUTATED	2	59	4	23
DEL PEAK 8(4P16.3) WILD-TYPE	53	103	112	159

Figure S382. Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S383. Gene #57: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 8(4P16.3) MUTATED	10	48	21
DEL PEAK 8(4P16.3) WILD-TYPE	111	129	73

Figure S383. Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.096

Table S384. Gene #57: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 8(4P16.3) MUTATED	48	9	22
DEL PEAK 8(4P16.3) WILD-TYPE	123	99	91

Figure S384. Get High-res Image Gene #57: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.31' versus 'CN_CNMF'

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

Table S385. Gene #58: 'del_4p15.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 9(4P15.31) MUTATED	3	13	76	1	2
DEL PEAK 9(4P15.31) WILD-TYPE	302	35	78	11	3

Figure S385. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.31' versus 'METHLYATION_CNMF'

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

Table S386. Gene #58: 'del_4p15.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 9(4P15.31) MUTATED	64	14	6
DEL PEAK 9(4P15.31) WILD-TYPE	94	72	160

Figure S386. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.31' versus 'MRNASEQ_CNMF'

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

Table S387. Gene #58: 'del_4p15.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 9(4P15.31) MUTATED	81	6	8
DEL PEAK 9(4P15.31) WILD-TYPE	143	144	137

Figure S387. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S388. Gene #58: 'del_4p15.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 9(4P15.31) MUTATED	68	20	7
DEL PEAK 9(4P15.31) WILD-TYPE	95	193	136

Figure S388. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_CNMF'

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

Table S389. Gene #58: 'del_4p15.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 9(4P15.31) MUTATED	8	76	9
DEL PEAK 9(4P15.31) WILD-TYPE	133	143	146

Figure S389. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S390. Gene #58: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 9(4P15.31) MUTATED	2	64	3	24
DEL PEAK 9(4P15.31) WILD-TYPE	53	98	113	158

Figure S390. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.31' versus 'MIRSEQ_MATURE_CNMF'

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

Table S391. Gene #58: 'del_4p15.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 9(4P15.31) MUTATED	9	54	21
DEL PEAK 9(4P15.31) WILD-TYPE	112	123	73

Figure S391. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S392. Gene #58: 'del_4p15.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 9(4P15.31) MUTATED	51	8	25
DEL PEAK 9(4P15.31) WILD-TYPE	120	100	88

Figure S392. Get High-res Image Gene #58: 'del_4p15.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.068

Table S393. Gene #59: '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 S393. Get High-res Image Gene #59: '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 S394. Gene #59: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 10(4Q22.1) MUTATED	2	9	88	1	2
DEL PEAK 10(4Q22.1) WILD-TYPE	303	39	66	11	3

Figure S394. Get High-res Image Gene #59: '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 S395. Gene #59: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 10(4Q22.1) MUTATED	67	16	5
DEL PEAK 10(4Q22.1) WILD-TYPE	91	70	161

Figure S395. Get High-res Image Gene #59: '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 S396. Gene #59: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 10(4Q22.1) MUTATED	90	6	6
DEL PEAK 10(4Q22.1) WILD-TYPE	134	144	139

Figure S396. Get High-res Image Gene #59: '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 S397. Gene #59: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 10(4Q22.1) MUTATED	76	20	6
DEL PEAK 10(4Q22.1) WILD-TYPE	87	193	137

Figure S397. Get High-res Image Gene #59: '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 S398. Gene #59: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 10(4Q22.1) MUTATED	6	85	8
DEL PEAK 10(4Q22.1) WILD-TYPE	135	134	147

Figure S398. Get High-res Image Gene #59: '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 S399. Gene #59: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 10(4Q22.1) MUTATED	1	75	2	21
DEL PEAK 10(4Q22.1) WILD-TYPE	54	87	114	161

Figure S399. Get High-res Image Gene #59: '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 S400. Gene #59: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 10(4Q22.1) MUTATED	6	55	27
DEL PEAK 10(4Q22.1) WILD-TYPE	115	122	67

Figure S400. Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S401. Gene #59: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 10(4Q22.1) MUTATED	50	6	32
DEL PEAK 10(4Q22.1) WILD-TYPE	121	102	81

Figure S401. Get High-res Image Gene #59: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.068

Table S402. Gene #60: '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 S402. Get High-res Image Gene #60: '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 S403. Gene #60: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 11(4Q34.3) MUTATED	6	10	106	1	2
DEL PEAK 11(4Q34.3) WILD-TYPE	299	38	48	11	3

Figure S403. Get High-res Image Gene #60: '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 S404. Gene #60: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 11(4Q34.3) MUTATED	76	22	11
DEL PEAK 11(4Q34.3) WILD-TYPE	82	64	155

Figure S404. Get High-res Image Gene #60: '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 S405. Gene #60: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 11(4Q34.3) MUTATED	109	9	7
DEL PEAK 11(4Q34.3) WILD-TYPE	115	141	138

Figure S405. Get High-res Image Gene #60: '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 S406. Gene #60: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 11(4Q34.3) MUTATED	91	27	7
DEL PEAK 11(4Q34.3) WILD-TYPE	72	186	136

Figure S406. Get High-res Image Gene #60: '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 S407. Gene #60: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 11(4Q34.3) MUTATED	16	97	9
DEL PEAK 11(4Q34.3) WILD-TYPE	125	122	146

Figure S407. Get High-res Image Gene #60: '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 S408. Gene #60: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 11(4Q34.3) MUTATED	2	85	5	30
DEL PEAK 11(4Q34.3) WILD-TYPE	53	77	111	152

Figure S408. Get High-res Image Gene #60: '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 S409. Gene #60: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 11(4Q34.3) MUTATED	10	66	32
DEL PEAK 11(4Q34.3) WILD-TYPE	111	111	62

Figure S409. Get High-res Image Gene #60: '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 S410. Gene #60: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 11(4Q34.3) MUTATED	61	9	38
DEL PEAK 11(4Q34.3) WILD-TYPE	110	99	75

Figure S410. Get High-res Image Gene #60: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

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

Table S411. Gene #61: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 12(5Q11.2) MUTATED	0	12	92	1	1
DEL PEAK 12(5Q11.2) WILD-TYPE	305	36	62	11	4

Figure S411. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

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

Table S412. Gene #61: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 12(5Q11.2) MUTATED	69	15	8
DEL PEAK 12(5Q11.2) WILD-TYPE	89	71	158

Figure S412. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'RPPA_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.14

Table S413. Gene #61: 'del_5q11.2' 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 12(5Q11.2) MUTATED	6	9	1	0	0	6
DEL PEAK 12(5Q11.2) WILD-TYPE	35	28	38	12	41	18

Figure S413. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q11.2' versus 'MRNASEQ_CNMF'

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

Table S414. Gene #61: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 12(5Q11.2) MUTATED	91	5	9
DEL PEAK 12(5Q11.2) WILD-TYPE	133	145	136

Figure S414. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S415. Gene #61: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 12(5Q11.2) MUTATED	75	19	11
DEL PEAK 12(5Q11.2) WILD-TYPE	88	194	132

Figure S415. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

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

Table S416. Gene #61: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 12(5Q11.2) MUTATED	10	84	11
DEL PEAK 12(5Q11.2) WILD-TYPE	131	135	144

Figure S416. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S417. Gene #61: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 12(5Q11.2) MUTATED	1	71	6	27
DEL PEAK 12(5Q11.2) WILD-TYPE	54	91	110	155

Figure S417. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S418. Gene #61: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 12(5Q11.2) MUTATED	11	61	19
DEL PEAK 12(5Q11.2) WILD-TYPE	110	116	75

Figure S418. Get High-res Image Gene #61: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S419. Gene #61: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 12(5Q11.2) MUTATED	56	11	24
DEL PEAK 12(5Q11.2) WILD-TYPE	115	97	89

Figure S419. Get High-res Image Gene #61: 'del_5q11.2' 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 S420. Gene #62: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 13(6Q26) MUTATED	4	4	37	0	0
DEL PEAK 13(6Q26) WILD-TYPE	301	44	117	12	5

Figure S420. Get High-res Image Gene #62: '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 S421. Gene #62: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 13(6Q26) MUTATED	30	8	1
DEL PEAK 13(6Q26) WILD-TYPE	128	78	165

Figure S421. Get High-res Image Gene #62: '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 S422. Gene #62: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 13(6Q26) MUTATED	41	2	2
DEL PEAK 13(6Q26) WILD-TYPE	183	148	143

Figure S422. Get High-res Image Gene #62: '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 S423. Gene #62: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 13(6Q26) MUTATED	37	7	1
DEL PEAK 13(6Q26) WILD-TYPE	126	206	142

Figure S423. Get High-res Image Gene #62: '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 S424. Gene #62: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 13(6Q26) MUTATED	6	35	3
DEL PEAK 13(6Q26) WILD-TYPE	135	184	152

Figure S424. Get High-res Image Gene #62: '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 S425. Gene #62: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 13(6Q26) MUTATED	0	34	1	9
DEL PEAK 13(6Q26) WILD-TYPE	55	128	115	173

Figure S425. Get High-res Image Gene #62: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.24

Table S426. Gene #63: '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	7	0	0
DEL PEAK 14(7P22.3) WILD-TYPE	14	10	12	10

Figure S426. Get High-res Image Gene #63: '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 S427. Gene #63: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 14(7P22.3) MUTATED	4	2	63	0	1
DEL PEAK 14(7P22.3) WILD-TYPE	301	46	91	12	4

Figure S427. Get High-res Image Gene #63: '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 S428. Gene #63: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 14(7P22.3) MUTATED	43	14	4
DEL PEAK 14(7P22.3) WILD-TYPE	115	72	162

Figure S428. Get High-res Image Gene #63: '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 S429. Gene #63: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 14(7P22.3) MUTATED	64	2	4
DEL PEAK 14(7P22.3) WILD-TYPE	160	148	141

Figure S429. Get High-res Image Gene #63: '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 S430. Gene #63: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 14(7P22.3) MUTATED	58	8	4
DEL PEAK 14(7P22.3) WILD-TYPE	105	205	139

Figure S430. Get High-res Image Gene #63: '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 S431. Gene #63: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 14(7P22.3) MUTATED	5	58	6
DEL PEAK 14(7P22.3) WILD-TYPE	136	161	149

Figure S431. Get High-res Image Gene #63: '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 S432. Gene #63: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 14(7P22.3) MUTATED	0	52	3	14
DEL PEAK 14(7P22.3) WILD-TYPE	55	110	113	168

Figure S432. Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.072

Table S433. Gene #63: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 14(7P22.3) MUTATED	5	36	17
DEL PEAK 14(7P22.3) WILD-TYPE	116	141	77

Figure S433. Get High-res Image Gene #63: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'CN_CNMF'

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

Table S434. Gene #64: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 15(7Q11.22) MUTATED	0	0	40	0	1
DEL PEAK 15(7Q11.22) WILD-TYPE	305	48	114	12	4

Figure S434. Get High-res Image Gene #64: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'METHLYATION_CNMF'

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

Table S435. Gene #64: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 15(7Q11.22) MUTATED	27	8	3
DEL PEAK 15(7Q11.22) WILD-TYPE	131	78	163

Figure S435. Get High-res Image Gene #64: '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 S436. Gene #64: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 15(7Q11.22) MUTATED	39	0	2
DEL PEAK 15(7Q11.22) WILD-TYPE	185	150	143

Figure S436. Get High-res Image Gene #64: '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 S437. Gene #64: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 15(7Q11.22) MUTATED	31	7	3
DEL PEAK 15(7Q11.22) WILD-TYPE	132	206	140

Figure S437. Get High-res Image Gene #64: '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 S438. Gene #64: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 15(7Q11.22) MUTATED	3	33	4
DEL PEAK 15(7Q11.22) WILD-TYPE	138	186	151

Figure S438. Get High-res Image Gene #64: '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 S439. Gene #64: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 15(7Q11.22) MUTATED	0	31	3	6
DEL PEAK 15(7Q11.22) WILD-TYPE	55	131	113	176

Figure S439. Get High-res Image Gene #64: '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 S440. Gene #65: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 16(7Q31.1) MUTATED	0	0	52	0	1
DEL PEAK 16(7Q31.1) WILD-TYPE	305	48	102	12	4

Figure S440. Get High-res Image Gene #65: '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 S441. Gene #65: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 16(7Q31.1) MUTATED	36	11	1
DEL PEAK 16(7Q31.1) WILD-TYPE	122	75	165

Figure S441. Get High-res Image Gene #65: '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 S442. Gene #65: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 16(7Q31.1) MUTATED	52	0	1
DEL PEAK 16(7Q31.1) WILD-TYPE	172	150	144

Figure S442. Get High-res Image Gene #65: '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 S443. Gene #65: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 16(7Q31.1) MUTATED	46	5	2
DEL PEAK 16(7Q31.1) WILD-TYPE	117	208	141

Figure S443. Get High-res Image Gene #65: '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 S444. Gene #65: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 16(7Q31.1) MUTATED	2	46	4
DEL PEAK 16(7Q31.1) WILD-TYPE	139	173	151

Figure S444. Get High-res Image Gene #65: '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 S445. Gene #65: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 16(7Q31.1) MUTATED	0	44	3	5
DEL PEAK 16(7Q31.1) WILD-TYPE	55	118	113	177

Figure S445. Get High-res Image Gene #65: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

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

Table S446. Gene #66: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 17(7Q36.1) MUTATED	1	1	59	0	1
DEL PEAK 17(7Q36.1) WILD-TYPE	304	47	95	12	4

Figure S446. Get High-res Image Gene #66: '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 S447. Gene #66: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 17(7Q36.1) MUTATED	40	12	1
DEL PEAK 17(7Q36.1) WILD-TYPE	118	74	165

Figure S447. Get High-res Image Gene #66: '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 S448. Gene #66: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 17(7Q36.1) MUTATED	61	0	1
DEL PEAK 17(7Q36.1) WILD-TYPE	163	150	144

Figure S448. Get High-res Image Gene #66: '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 S449. Gene #66: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 17(7Q36.1) MUTATED	56	4	2
DEL PEAK 17(7Q36.1) WILD-TYPE	107	209	141

Figure S449. Get High-res Image Gene #66: '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 S450. Gene #66: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 17(7Q36.1) MUTATED	2	55	4
DEL PEAK 17(7Q36.1) WILD-TYPE	139	164	151

Figure S450. Get High-res Image Gene #66: '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 S451. Gene #66: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 17(7Q36.1) MUTATED	0	52	3	6
DEL PEAK 17(7Q36.1) WILD-TYPE	55	110	113	176

Figure S451. Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.072

Table S452. Gene #66: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 17(7Q36.1) MUTATED	4	33	13
DEL PEAK 17(7Q36.1) WILD-TYPE	117	144	81

Figure S452. Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.19

Table S453. Gene #66: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 17(7Q36.1) MUTATED	32	4	14
DEL PEAK 17(7Q36.1) WILD-TYPE	139	104	99

Figure S453. Get High-res Image Gene #66: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

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

Table S454. Gene #67: '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 S454. Get High-res Image Gene #67: '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 S455. Gene #67: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 18(8P23.2) MUTATED	8	7	97	0	1
DEL PEAK 18(8P23.2) WILD-TYPE	297	41	57	12	4

Figure S455. Get High-res Image Gene #67: '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 S456. Gene #67: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 18(8P23.2) MUTATED	78	16	5
DEL PEAK 18(8P23.2) WILD-TYPE	80	70	161

Figure S456. Get High-res Image Gene #67: '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 S457. Gene #67: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 18(8P23.2) MUTATED	102	6	4
DEL PEAK 18(8P23.2) WILD-TYPE	122	144	141

Figure S457. Get High-res Image Gene #67: '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 S458. Gene #67: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 18(8P23.2) MUTATED	90	16	6
DEL PEAK 18(8P23.2) WILD-TYPE	73	197	137

Figure S458. Get High-res Image Gene #67: '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 S459. Gene #67: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 18(8P23.2) MUTATED	4	99	7
DEL PEAK 18(8P23.2) WILD-TYPE	137	120	148

Figure S459. Get High-res Image Gene #67: '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 S460. Gene #67: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 18(8P23.2) MUTATED	2	87	4	17
DEL PEAK 18(8P23.2) WILD-TYPE	53	75	112	165

Figure S460. Get High-res Image Gene #67: '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 S461. Gene #67: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 18(8P23.2) MUTATED	5	65	24
DEL PEAK 18(8P23.2) WILD-TYPE	116	112	70

Figure S461. Get High-res Image Gene #67: '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 S462. Gene #67: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 18(8P23.2) MUTATED	57	5	32
DEL PEAK 18(8P23.2) WILD-TYPE	114	103	81

Figure S462. Get High-res Image Gene #67: '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 S463. Gene #68: '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 S463. Get High-res Image Gene #68: '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 S464. Gene #68: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 19(8P21.2) MUTATED	5	5	100	0	1
DEL PEAK 19(8P21.2) WILD-TYPE	300	43	54	12	4

Figure S464. Get High-res Image Gene #68: '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 S465. Gene #68: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 19(8P21.2) MUTATED	80	15	2
DEL PEAK 19(8P21.2) WILD-TYPE	78	71	164

Figure S465. Get High-res Image Gene #68: '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 S466. Gene #68: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 19(8P21.2) MUTATED	104	5	1
DEL PEAK 19(8P21.2) WILD-TYPE	120	145	144

Figure S466. Get High-res Image Gene #68: '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 S467. Gene #68: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 19(8P21.2) MUTATED	93	14	3
DEL PEAK 19(8P21.2) WILD-TYPE	70	199	140

Figure S467. Get High-res Image Gene #68: '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 S468. Gene #68: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 19(8P21.2) MUTATED	4	101	3
DEL PEAK 19(8P21.2) WILD-TYPE	137	118	152

Figure S468. Get High-res Image Gene #68: '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 S469. Gene #68: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 19(8P21.2) MUTATED	2	90	1	15
DEL PEAK 19(8P21.2) WILD-TYPE	53	72	115	167

Figure S469. Get High-res Image Gene #68: '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 S470. Gene #68: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 19(8P21.2) MUTATED	2	66	25
DEL PEAK 19(8P21.2) WILD-TYPE	119	111	69

Figure S470. Get High-res Image Gene #68: '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 S471. Gene #68: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 19(8P21.2) MUTATED	60	3	30
DEL PEAK 19(8P21.2) WILD-TYPE	111	105	83

Figure S471. Get High-res Image Gene #68: '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 S472. Gene #69: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 20(9P23) MUTATED	2	13	59	0	1
DEL PEAK 20(9P23) WILD-TYPE	303	35	95	12	4

Figure S472. Get High-res Image Gene #69: '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 S473. Gene #69: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 20(9P23) MUTATED	40	18	8
DEL PEAK 20(9P23) WILD-TYPE	118	68	158

Figure S473. Get High-res Image Gene #69: '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 S474. Gene #69: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 20(9P23) MUTATED	59	5	11
DEL PEAK 20(9P23) WILD-TYPE	165	145	134

Figure S474. Get High-res Image Gene #69: '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 S475. Gene #69: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 20(9P23) MUTATED	51	13	11
DEL PEAK 20(9P23) WILD-TYPE	112	200	132

Figure S475. Get High-res Image Gene #69: '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 S476. Gene #69: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 20(9P23) MUTATED	6	53	15
DEL PEAK 20(9P23) WILD-TYPE	135	166	140

Figure S476. Get High-res Image Gene #69: '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 S477. Gene #69: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 20(9P23) MUTATED	1	48	10	15
DEL PEAK 20(9P23) WILD-TYPE	54	114	106	167

Figure S477. Get High-res Image Gene #69: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S478. Gene #70: '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 S478. Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S479. Gene #70: '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 S479. Get High-res Image Gene #70: '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 S480. Gene #70: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 21(9Q21.2) MUTATED	3	19	100	0	1
DEL PEAK 21(9Q21.2) WILD-TYPE	302	29	54	12	4

Figure S480. Get High-res Image Gene #70: '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 S481. Gene #70: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 21(9Q21.2) MUTATED	72	20	15
DEL PEAK 21(9Q21.2) WILD-TYPE	86	66	151

Figure S481. Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.2' versus 'RPPA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.16

Table S482. Gene #70: '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 S482. Get High-res Image Gene #70: '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 S483. Gene #70: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 21(9Q21.2) MUTATED	99	8	16
DEL PEAK 21(9Q21.2) WILD-TYPE	125	142	129

Figure S483. Get High-res Image Gene #70: '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 S484. Gene #70: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 21(9Q21.2) MUTATED	86	21	16
DEL PEAK 21(9Q21.2) WILD-TYPE	77	192	127

Figure S484. Get High-res Image Gene #70: '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 S485. Gene #70: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 21(9Q21.2) MUTATED	11	91	18
DEL PEAK 21(9Q21.2) WILD-TYPE	130	128	137

Figure S485. Get High-res Image Gene #70: '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 S486. Gene #70: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 21(9Q21.2) MUTATED	2	80	12	26
DEL PEAK 21(9Q21.2) WILD-TYPE	53	82	104	156

Figure S486. Get High-res Image Gene #70: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.023

Table S487. Gene #71: '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 S487. Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S488. Gene #71: '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 S488. Get High-res Image Gene #71: '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 S489. Gene #71: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 22(9Q34.2) MUTATED	4	19	105	0	0
DEL PEAK 22(9Q34.2) WILD-TYPE	301	29	49	12	5

Figure S489. Get High-res Image Gene #71: '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 S490. Gene #71: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 22(9Q34.2) MUTATED	74	23	13
DEL PEAK 22(9Q34.2) WILD-TYPE	84	63	153

Figure S490. Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'MRNASEQ_CNMF'

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

Table S491. Gene #71: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 22(9Q34.2) MUTATED	102	9	16
DEL PEAK 22(9Q34.2) WILD-TYPE	122	141	129

Figure S491. Get High-res Image Gene #71: '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 S492. Gene #71: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 22(9Q34.2) MUTATED	86	24	17
DEL PEAK 22(9Q34.2) WILD-TYPE	77	189	126

Figure S492. Get High-res Image Gene #71: '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 S493. Gene #71: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 22(9Q34.2) MUTATED	11	95	19
DEL PEAK 22(9Q34.2) WILD-TYPE	130	124	136

Figure S493. Get High-res Image Gene #71: '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 S494. Gene #71: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 22(9Q34.2) MUTATED	2	80	12	31
DEL PEAK 22(9Q34.2) WILD-TYPE	53	82	104	151

Figure S494. Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.058

Table S495. Gene #71: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 22(9Q34.2) MUTATED	17	64	27
DEL PEAK 22(9Q34.2) WILD-TYPE	104	113	67

Figure S495. Get High-res Image Gene #71: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

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

Table S496. Gene #72: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 23(10Q23.31) MUTATED	5	4	64	0	0
DEL PEAK 23(10Q23.31) WILD-TYPE	300	44	90	12	5

Figure S496. Get High-res Image Gene #72: '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 S497. Gene #72: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 23(10Q23.31) MUTATED	45	13	6
DEL PEAK 23(10Q23.31) WILD-TYPE	113	73	160

Figure S497. Get High-res Image Gene #72: '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 S498. Gene #72: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 23(10Q23.31) MUTATED	60	5	7
DEL PEAK 23(10Q23.31) WILD-TYPE	164	145	138

Figure S498. Get High-res Image Gene #72: '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 S499. Gene #72: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 23(10Q23.31) MUTATED	49	15	8
DEL PEAK 23(10Q23.31) WILD-TYPE	114	198	135

Figure S499. Get High-res Image Gene #72: '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 S500. Gene #72: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 23(10Q23.31) MUTATED	7	57	8
DEL PEAK 23(10Q23.31) WILD-TYPE	134	162	147

Figure S500. Get High-res Image Gene #72: '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 S501. Gene #72: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 23(10Q23.31) MUTATED	1	45	7	19
DEL PEAK 23(10Q23.31) WILD-TYPE	54	117	109	163

Figure S501. Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.096

Table S502. Gene #72: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 23(10Q23.31) MUTATED	7	40	16
DEL PEAK 23(10Q23.31) WILD-TYPE	114	137	78

Figure S502. Get High-res Image Gene #72: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'CN_CNMF'

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

Table S503. Gene #73: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 24(11P15.5) MUTATED	1	13	83	0	2
DEL PEAK 24(11P15.5) WILD-TYPE	304	35	71	12	3

Figure S503. Get High-res Image Gene #73: '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 S504. Gene #73: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 24(11P15.5) MUTATED	66	18	6
DEL PEAK 24(11P15.5) WILD-TYPE	92	68	160

Figure S504. Get High-res Image Gene #73: '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 S505. Gene #73: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 24(11P15.5) MUTATED	83	4	11
DEL PEAK 24(11P15.5) WILD-TYPE	141	146	134

Figure S505. Get High-res Image Gene #73: '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 S506. Gene #73: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 24(11P15.5) MUTATED	70	16	12
DEL PEAK 24(11P15.5) WILD-TYPE	93	197	131

Figure S506. Get High-res Image Gene #73: '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 S507. Gene #73: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 24(11P15.5) MUTATED	8	77	13
DEL PEAK 24(11P15.5) WILD-TYPE	133	142	142

Figure S507. Get High-res Image Gene #73: '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 S508. Gene #73: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 24(11P15.5) MUTATED	1	67	10	20
DEL PEAK 24(11P15.5) WILD-TYPE	54	95	106	162

Figure S508. Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S509. Gene #73: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 24(11P15.5) MUTATED	13	61	17
DEL PEAK 24(11P15.5) WILD-TYPE	108	116	77

Figure S509. Get High-res Image Gene #73: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.072

Table S510. Gene #73: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 24(11P15.5) MUTATED	57	14	20
DEL PEAK 24(11P15.5) WILD-TYPE	114	94	93

Figure S510. Get High-res Image Gene #73: '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 S511. Gene #74: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 25(11Q14.1) MUTATED	1	12	51	0	2
DEL PEAK 25(11Q14.1) WILD-TYPE	304	36	103	12	3

Figure S511. Get High-res Image Gene #74: '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 S512. Gene #74: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 25(11Q14.1) MUTATED	47	10	5
DEL PEAK 25(11Q14.1) WILD-TYPE	111	76	161

Figure S512. Get High-res Image Gene #74: '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 S513. Gene #74: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 25(11Q14.1) MUTATED	56	2	7
DEL PEAK 25(11Q14.1) WILD-TYPE	168	148	138

Figure S513. Get High-res Image Gene #74: '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 S514. Gene #74: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 25(11Q14.1) MUTATED	51	8	6
DEL PEAK 25(11Q14.1) WILD-TYPE	112	205	137

Figure S514. Get High-res Image Gene #74: '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 S515. Gene #74: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 25(11Q14.1) MUTATED	5	52	9
DEL PEAK 25(11Q14.1) WILD-TYPE	136	167	146

Figure S515. Get High-res Image Gene #74: '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 S516. Gene #74: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 25(11Q14.1) MUTATED	0	49	5	12
DEL PEAK 25(11Q14.1) WILD-TYPE	55	113	111	170

Figure S516. Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.1

Table S517. Gene #74: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 25(11Q14.1) MUTATED	8	42	12
DEL PEAK 25(11Q14.1) WILD-TYPE	113	135	82

Figure S517. Get High-res Image Gene #74: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00053 (Fisher's exact test), Q value = 0.25

Table S518. Gene #74: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 25(11Q14.1) MUTATED	40	7	15
DEL PEAK 25(11Q14.1) WILD-TYPE	131	101	98

Figure S518. Get High-res Image Gene #74: '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 S519. Gene #75: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 26(11Q25) MUTATED	4	16	67	0	2
DEL PEAK 26(11Q25) WILD-TYPE	301	32	87	12	3

Figure S519. Get High-res Image Gene #75: '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 S520. Gene #75: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 26(11Q25) MUTATED	62	11	7
DEL PEAK 26(11Q25) WILD-TYPE	96	75	159

Figure S520. Get High-res Image Gene #75: '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 S521. Gene #75: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 26(11Q25) MUTATED	72	7	9
DEL PEAK 26(11Q25) WILD-TYPE	152	143	136

Figure S521. Get High-res Image Gene #75: '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 S522. Gene #75: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 26(11Q25) MUTATED	62	17	9
DEL PEAK 26(11Q25) WILD-TYPE	101	196	134

Figure S522. Get High-res Image Gene #75: '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 S523. Gene #75: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 26(11Q25) MUTATED	10	65	12
DEL PEAK 26(11Q25) WILD-TYPE	131	154	143

Figure S523. Get High-res Image Gene #75: '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 S524. Gene #75: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 26(11Q25) MUTATED	1	59	7	20
DEL PEAK 26(11Q25) WILD-TYPE	54	103	109	162

Figure S524. Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

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

Table S525. Gene #75: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 26(11Q25) MUTATED	10	52	18
DEL PEAK 26(11Q25) WILD-TYPE	111	125	76

Figure S525. Get High-res Image Gene #75: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.068

Table S526. Gene #75: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 26(11Q25) MUTATED	49	9	22
DEL PEAK 26(11Q25) WILD-TYPE	122	99	91

Figure S526. Get High-res Image Gene #75: '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 S527. Gene #76: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 27(12Q23.1) MUTATED	0	3	49	1	0
DEL PEAK 27(12Q23.1) WILD-TYPE	305	45	105	11	5

Figure S527. Get High-res Image Gene #76: '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 S528. Gene #76: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 27(12Q23.1) MUTATED	39	6	0
DEL PEAK 27(12Q23.1) WILD-TYPE	119	80	166

Figure S528. Get High-res Image Gene #76: '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 S529. Gene #76: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 27(12Q23.1) MUTATED	48	2	3
DEL PEAK 27(12Q23.1) WILD-TYPE	176	148	142

Figure S529. Get High-res Image Gene #76: '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 S530. Gene #76: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 27(12Q23.1) MUTATED	45	3	5
DEL PEAK 27(12Q23.1) WILD-TYPE	118	210	138

Figure S530. Get High-res Image Gene #76: '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 S531. Gene #76: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 27(12Q23.1) MUTATED	5	43	3
DEL PEAK 27(12Q23.1) WILD-TYPE	136	176	152

Figure S531. Get High-res Image Gene #76: '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 S532. Gene #76: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 27(12Q23.1) MUTATED	0	44	0	7
DEL PEAK 27(12Q23.1) WILD-TYPE	55	118	116	175

Figure S532. Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S533. Gene #76: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 27(12Q23.1) MUTATED	2	30	13
DEL PEAK 27(12Q23.1) WILD-TYPE	119	147	81

Figure S533. Get High-res Image Gene #76: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S534. Gene #76: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 27(12Q23.1) MUTATED	28	2	15
DEL PEAK 27(12Q23.1) WILD-TYPE	143	106	98

Figure S534. Get High-res Image Gene #76: '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 S535. Gene #77: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 28(12Q24.33) MUTATED	1	3	59	1	0
DEL PEAK 28(12Q24.33) WILD-TYPE	304	45	95	11	5

Figure S535. Get High-res Image Gene #77: '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 S536. Gene #77: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 28(12Q24.33) MUTATED	46	9	3
DEL PEAK 28(12Q24.33) WILD-TYPE	112	77	163

Figure S536. Get High-res Image Gene #77: '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 S537. Gene #77: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 28(12Q24.33) MUTATED	60	1	3
DEL PEAK 28(12Q24.33) WILD-TYPE	164	149	142

Figure S537. Get High-res Image Gene #77: '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 S538. Gene #77: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 28(12Q24.33) MUTATED	51	10	3
DEL PEAK 28(12Q24.33) WILD-TYPE	112	203	140

Figure S538. Get High-res Image Gene #77: '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 S539. Gene #77: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 28(12Q24.33) MUTATED	5	54	3
DEL PEAK 28(12Q24.33) WILD-TYPE	136	165	152

Figure S539. Get High-res Image Gene #77: '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 S540. Gene #77: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 28(12Q24.33) MUTATED	0	48	2	12
DEL PEAK 28(12Q24.33) WILD-TYPE	55	114	114	170

Figure S540. Get High-res Image Gene #77: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

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

Table S541. Gene #77: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 28(12Q24.33) MUTATED	4	43	11
DEL PEAK 28(12Q24.33) WILD-TYPE	117	134	83

Figure S541. Get High-res Image Gene #77: '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 S542. Gene #77: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 28(12Q24.33) MUTATED	40	4	14
DEL PEAK 28(12Q24.33) WILD-TYPE	131	104	99

Figure S542. Get High-res Image Gene #77: '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 S543. Gene #78: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 29(13Q11) MUTATED	2	19	73	1	1
DEL PEAK 29(13Q11) WILD-TYPE	303	29	81	11	4

Figure S543. Get High-res Image Gene #78: '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 S544. Gene #78: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 29(13Q11) MUTATED	55	17	10
DEL PEAK 29(13Q11) WILD-TYPE	103	69	156

Figure S544. Get High-res Image Gene #78: '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 S545. Gene #78: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 29(13Q11) MUTATED	74	7	15
DEL PEAK 29(13Q11) WILD-TYPE	150	143	130

Figure S545. Get High-res Image Gene #78: '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 S546. Gene #78: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 29(13Q11) MUTATED	60	21	15
DEL PEAK 29(13Q11) WILD-TYPE	103	192	128

Figure S546. Get High-res Image Gene #78: '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 S547. Gene #78: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 29(13Q11) MUTATED	13	69	13
DEL PEAK 29(13Q11) WILD-TYPE	128	150	142

Figure S547. Get High-res Image Gene #78: '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 S548. Gene #78: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 29(13Q11) MUTATED	1	61	8	25
DEL PEAK 29(13Q11) WILD-TYPE	54	101	108	157

Figure S548. Get High-res Image Gene #78: '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 S549. Gene #79: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 30(13Q14.2) MUTATED	3	21	77	1	1
DEL PEAK 30(13Q14.2) WILD-TYPE	302	27	77	11	4

Figure S549. Get High-res Image Gene #79: '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 S550. Gene #79: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 30(13Q14.2) MUTATED	57	20	13
DEL PEAK 30(13Q14.2) WILD-TYPE	101	66	153

Figure S550. Get High-res Image Gene #79: '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 S551. Gene #79: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 30(13Q14.2) MUTATED	77	8	18
DEL PEAK 30(13Q14.2) WILD-TYPE	147	142	127

Figure S551. Get High-res Image Gene #79: '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 S552. Gene #79: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 30(13Q14.2) MUTATED	59	26	18
DEL PEAK 30(13Q14.2) WILD-TYPE	104	187	125

Figure S552. Get High-res Image Gene #79: '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 S553. Gene #79: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 30(13Q14.2) MUTATED	16	69	17
DEL PEAK 30(13Q14.2) WILD-TYPE	125	150	138

Figure S553. Get High-res Image Gene #79: '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 S554. Gene #79: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 30(13Q14.2) MUTATED	1	59	11	31
DEL PEAK 30(13Q14.2) WILD-TYPE	54	103	105	151

Figure S554. Get High-res Image Gene #79: '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 S555. Gene #80: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 31(14Q13.1) MUTATED	2	6	58	1	2
DEL PEAK 31(14Q13.1) WILD-TYPE	303	42	96	11	3

Figure S555. Get High-res Image Gene #80: '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 S556. Gene #80: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 31(14Q13.1) MUTATED	47	8	5
DEL PEAK 31(14Q13.1) WILD-TYPE	111	78	161

Figure S556. Get High-res Image Gene #80: '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 S557. Gene #80: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 31(14Q13.1) MUTATED	58	4	6
DEL PEAK 31(14Q13.1) WILD-TYPE	166	146	139

Figure S557. Get High-res Image Gene #80: '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 S558. Gene #80: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 31(14Q13.1) MUTATED	51	11	6
DEL PEAK 31(14Q13.1) WILD-TYPE	112	202	137

Figure S558. Get High-res Image Gene #80: '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 S559. Gene #80: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 31(14Q13.1) MUTATED	10	53	5
DEL PEAK 31(14Q13.1) WILD-TYPE	131	166	150

Figure S559. Get High-res Image Gene #80: '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 S560. Gene #80: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 31(14Q13.1) MUTATED	0	48	3	17
DEL PEAK 31(14Q13.1) WILD-TYPE	55	114	113	165

Figure S560. Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.028

Table S561. Gene #80: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 31(14Q13.1) MUTATED	6	41	15
DEL PEAK 31(14Q13.1) WILD-TYPE	115	136	79

Figure S561. Get High-res Image Gene #80: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.17

Table S562. Gene #80: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 31(14Q13.1) MUTATED	39	6	17
DEL PEAK 31(14Q13.1) WILD-TYPE	132	102	96

Figure S562. Get High-res Image Gene #80: '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 S563. Gene #81: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 32(15Q15.1) MUTATED	5	18	110	0	2
DEL PEAK 32(15Q15.1) WILD-TYPE	300	30	44	12	3

Figure S563. Get High-res Image Gene #81: '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 S564. Gene #81: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 32(15Q15.1) MUTATED	84	23	12
DEL PEAK 32(15Q15.1) WILD-TYPE	74	63	154

Figure S564. Get High-res Image Gene #81: '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 S565. Gene #81: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 32(15Q15.1) MUTATED	114	10	11
DEL PEAK 32(15Q15.1) WILD-TYPE	110	140	134

Figure S565. Get High-res Image Gene #81: '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 S566. Gene #81: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 32(15Q15.1) MUTATED	94	29	12
DEL PEAK 32(15Q15.1) WILD-TYPE	69	184	131

Figure S566. Get High-res Image Gene #81: '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 S567. Gene #81: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 32(15Q15.1) MUTATED	14	106	13
DEL PEAK 32(15Q15.1) WILD-TYPE	127	113	142

Figure S567. Get High-res Image Gene #81: '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 S568. Gene #81: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 32(15Q15.1) MUTATED	2	90	8	33
DEL PEAK 32(15Q15.1) WILD-TYPE	53	72	108	149

Figure S568. Get High-res Image Gene #81: '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 S569. Gene #81: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 32(15Q15.1) MUTATED	14	70	32
DEL PEAK 32(15Q15.1) WILD-TYPE	107	107	62

Figure S569. Get High-res Image Gene #81: '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 S570. Gene #81: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 32(15Q15.1) MUTATED	68	14	34
DEL PEAK 32(15Q15.1) WILD-TYPE	103	94	79

Figure S570. Get High-res Image Gene #81: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.22

Table S571. Gene #82: '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 S571. Get High-res Image Gene #82: '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 S572. Gene #82: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 33(15Q23) MUTATED	4	15	88	0	3
DEL PEAK 33(15Q23) WILD-TYPE	301	33	66	12	2

Figure S572. Get High-res Image Gene #82: '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 S573. Gene #82: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 33(15Q23) MUTATED	72	16	8
DEL PEAK 33(15Q23) WILD-TYPE	86	70	158

Figure S573. Get High-res Image Gene #82: '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 S574. Gene #82: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 33(15Q23) MUTATED	93	9	8
DEL PEAK 33(15Q23) WILD-TYPE	131	141	137

Figure S574. Get High-res Image Gene #82: '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 S575. Gene #82: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 33(15Q23) MUTATED	81	21	8
DEL PEAK 33(15Q23) WILD-TYPE	82	192	135

Figure S575. Get High-res Image Gene #82: '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 S576. Gene #82: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 33(15Q23) MUTATED	13	85	10
DEL PEAK 33(15Q23) WILD-TYPE	128	134	145

Figure S576. Get High-res Image Gene #82: '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 S577. Gene #82: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 33(15Q23) MUTATED	2	75	5	26
DEL PEAK 33(15Q23) WILD-TYPE	53	87	111	156

Figure S577. Get High-res Image Gene #82: '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 S578. Gene #82: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 33(15Q23) MUTATED	10	64	20
DEL PEAK 33(15Q23) WILD-TYPE	111	113	74

Figure S578. Get High-res Image Gene #82: '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 S579. Gene #82: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 33(15Q23) MUTATED	59	9	26
DEL PEAK 33(15Q23) WILD-TYPE	112	99	87

Figure S579. Get High-res Image Gene #82: '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 S580. Gene #83: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 34(16P13.3) MUTATED	2	8	78	0	0
DEL PEAK 34(16P13.3) WILD-TYPE	303	40	76	12	5

Figure S580. Get High-res Image Gene #83: '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 S581. Gene #83: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 34(16P13.3) MUTATED	58	17	4
DEL PEAK 34(16P13.3) WILD-TYPE	100	69	162

Figure S581. Get High-res Image Gene #83: '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 S582. Gene #83: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 34(16P13.3) MUTATED	79	2	7
DEL PEAK 34(16P13.3) WILD-TYPE	145	148	138

Figure S582. Get High-res Image Gene #83: '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 S583. Gene #83: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 34(16P13.3) MUTATED	68	13	7
DEL PEAK 34(16P13.3) WILD-TYPE	95	200	136

Figure S583. Get High-res Image Gene #83: '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 S584. Gene #83: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 34(16P13.3) MUTATED	7	72	7
DEL PEAK 34(16P13.3) WILD-TYPE	134	147	148

Figure S584. Get High-res Image Gene #83: '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 S585. Gene #83: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 34(16P13.3) MUTATED	0	66	5	15
DEL PEAK 34(16P13.3) WILD-TYPE	55	96	111	167

Figure S585. Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.054

Table S586. Gene #83: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 34(16P13.3) MUTATED	9	48	21
DEL PEAK 34(16P13.3) WILD-TYPE	112	129	73

Figure S586. Get High-res Image Gene #83: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.017

Table S587. Gene #83: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 34(16P13.3) MUTATED	47	7	24
DEL PEAK 34(16P13.3) WILD-TYPE	124	101	89

Figure S587. Get High-res Image Gene #83: '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 = 0.043

Table S588. Gene #84: '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 S588. Get High-res Image Gene #84: '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 S589. Gene #84: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 35(16Q21) MUTATED	15	14	121	0	0
DEL PEAK 35(16Q21) WILD-TYPE	290	34	33	12	5

Figure S589. Get High-res Image Gene #84: '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 S590. Gene #84: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 35(16Q21) MUTATED	89	26	16
DEL PEAK 35(16Q21) WILD-TYPE	69	60	150

Figure S590. Get High-res Image Gene #84: '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 S591. Gene #84: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 35(16Q21) MUTATED	119	15	15
DEL PEAK 35(16Q21) WILD-TYPE	105	135	130

Figure S591. Get High-res Image Gene #84: '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 S592. Gene #84: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 35(16Q21) MUTATED	100	34	15
DEL PEAK 35(16Q21) WILD-TYPE	63	179	128

Figure S592. Get High-res Image Gene #84: '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 S593. Gene #84: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 35(16Q21) MUTATED	21	108	17
DEL PEAK 35(16Q21) WILD-TYPE	120	111	138

Figure S593. Get High-res Image Gene #84: '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 S594. Gene #84: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 35(16Q21) MUTATED	7	95	12	32
DEL PEAK 35(16Q21) WILD-TYPE	48	67	104	150

Figure S594. Get High-res Image Gene #84: '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 S595. Gene #84: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 35(16Q21) MUTATED	18	79	32
DEL PEAK 35(16Q21) WILD-TYPE	103	98	62

Figure S595. Get High-res Image Gene #84: '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 S596. Gene #84: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 35(16Q21) MUTATED	76	18	35
DEL PEAK 35(16Q21) WILD-TYPE	95	90	78

Figure S596. Get High-res Image Gene #84: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.13

Table S597. Gene #85: '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 36(16Q23.1) MUTATED	4	7	0	0	1
DEL PEAK 36(16Q23.1) WILD-TYPE	10	2	7	7	15

Figure S597. Get High-res Image Gene #85: '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 S598. Gene #85: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 36(16Q23.1) MUTATED	20	14	127	0	0
DEL PEAK 36(16Q23.1) WILD-TYPE	285	34	27	12	5

Figure S598. Get High-res Image Gene #85: '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 S599. Gene #85: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 36(16Q23.1) MUTATED	91	27	19
DEL PEAK 36(16Q23.1) WILD-TYPE	67	59	147

Figure S599. Get High-res Image Gene #85: '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 S600. Gene #85: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 36(16Q23.1) MUTATED	128	17	16
DEL PEAK 36(16Q23.1) WILD-TYPE	96	133	129

Figure S600. Get High-res Image Gene #85: '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 S601. Gene #85: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 36(16Q23.1) MUTATED	106	39	16
DEL PEAK 36(16Q23.1) WILD-TYPE	57	174	127

Figure S601. Get High-res Image Gene #85: '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 S602. Gene #85: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 36(16Q23.1) MUTATED	22	115	19
DEL PEAK 36(16Q23.1) WILD-TYPE	119	104	136

Figure S602. Get High-res Image Gene #85: '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 S603. Gene #85: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 36(16Q23.1) MUTATED	7	103	13	33
DEL PEAK 36(16Q23.1) WILD-TYPE	48	59	103	149

Figure S603. Get High-res Image Gene #85: '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 S604. Gene #85: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 36(16Q23.1) MUTATED	18	81	36
DEL PEAK 36(16Q23.1) WILD-TYPE	103	96	58

Figure S604. Get High-res Image Gene #85: '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 S605. Gene #85: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 36(16Q23.1) MUTATED	77	17	41
DEL PEAK 36(16Q23.1) WILD-TYPE	94	91	72

Figure S605. Get High-res Image Gene #85: '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 S606. Gene #86: '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 37(17P13.3) MUTATED	1	7	1	0	0
DEL PEAK 37(17P13.3) WILD-TYPE	13	2	6	7	16

Figure S606. Get High-res Image Gene #86: '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 S607. Gene #86: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 37(17P13.3) MUTATED	3	14	98	0	0
DEL PEAK 37(17P13.3) WILD-TYPE	302	34	56	12	5

Figure S607. Get High-res Image Gene #86: '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 S608. Gene #86: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 37(17P13.3) MUTATED	65	20	12
DEL PEAK 37(17P13.3) WILD-TYPE	93	66	154

Figure S608. Get High-res Image Gene #86: '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 S609. Gene #86: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 37(17P13.3) MUTATED	94	6	14
DEL PEAK 37(17P13.3) WILD-TYPE	130	144	131

Figure S609. Get High-res Image Gene #86: '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 S610. Gene #86: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 37(17P13.3) MUTATED	80	18	16
DEL PEAK 37(17P13.3) WILD-TYPE	83	195	127

Figure S610. Get High-res Image Gene #86: '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 S611. Gene #86: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 37(17P13.3) MUTATED	11	85	16
DEL PEAK 37(17P13.3) WILD-TYPE	130	134	139

Figure S611. Get High-res Image Gene #86: '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 S612. Gene #86: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 37(17P13.3) MUTATED	2	72	11	27
DEL PEAK 37(17P13.3) WILD-TYPE	53	90	105	155

Figure S612. Get High-res Image Gene #86: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

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

Table S613. Gene #87: '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 38(17P11.2) MUTATED	0	8	1	0	0
DEL PEAK 38(17P11.2) WILD-TYPE	14	1	6	7	16

Figure S613. Get High-res Image Gene #87: '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 S614. Gene #87: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 38(17P11.2) MUTATED	4	13	105	0	0
DEL PEAK 38(17P11.2) WILD-TYPE	301	35	49	12	5

Figure S614. Get High-res Image Gene #87: '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 S615. Gene #87: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 38(17P11.2) MUTATED	73	21	12
DEL PEAK 38(17P11.2) WILD-TYPE	85	65	154

Figure S615. Get High-res Image Gene #87: '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 S616. Gene #87: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 38(17P11.2) MUTATED	104	5	13
DEL PEAK 38(17P11.2) WILD-TYPE	120	145	132

Figure S616. Get High-res Image Gene #87: '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 S617. Gene #87: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 38(17P11.2) MUTATED	89	18	15
DEL PEAK 38(17P11.2) WILD-TYPE	74	195	128

Figure S617. Get High-res Image Gene #87: '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 S618. Gene #87: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 38(17P11.2) MUTATED	10	91	17
DEL PEAK 38(17P11.2) WILD-TYPE	131	128	138

Figure S618. Get High-res Image Gene #87: '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 S619. Gene #87: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 38(17P11.2) MUTATED	1	80	12	25
DEL PEAK 38(17P11.2) WILD-TYPE	54	82	104	157

Figure S619. Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.22

Table S620. Gene #87: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 38(17P11.2) MUTATED	17	60	26
DEL PEAK 38(17P11.2) WILD-TYPE	104	117	68

Figure S620. Get High-res Image Gene #87: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.068

Table S621. Gene #88: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 39(17P11.2) MUTATED	0	8	0	0
DEL PEAK 39(17P11.2) WILD-TYPE	14	9	12	10

Figure S621. Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

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

Table S622. Gene #88: '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	1	7	0	0	0
DEL PEAK 39(17P11.2) WILD-TYPE	13	2	7	7	16

Figure S622. Get High-res Image Gene #88: '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 S623. Gene #88: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 39(17P11.2) MUTATED	2	12	102	0	0
DEL PEAK 39(17P11.2) WILD-TYPE	303	36	52	12	5

Figure S623. Get High-res Image Gene #88: '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 S624. Gene #88: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 39(17P11.2) MUTATED	70	21	11
DEL PEAK 39(17P11.2) WILD-TYPE	88	65	155

Figure S624. Get High-res Image Gene #88: '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 S625. Gene #88: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 39(17P11.2) MUTATED	99	5	12
DEL PEAK 39(17P11.2) WILD-TYPE	125	145	133

Figure S625. Get High-res Image Gene #88: '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 S626. Gene #88: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 39(17P11.2) MUTATED	83	19	14
DEL PEAK 39(17P11.2) WILD-TYPE	80	194	129

Figure S626. Get High-res Image Gene #88: '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 S627. Gene #88: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 39(17P11.2) MUTATED	9	88	16
DEL PEAK 39(17P11.2) WILD-TYPE	132	131	139

Figure S627. Get High-res Image Gene #88: '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 S628. Gene #88: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 39(17P11.2) MUTATED	1	76	11	25
DEL PEAK 39(17P11.2) WILD-TYPE	54	86	105	157

Figure S628. Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.096

Table S629. Gene #88: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 39(17P11.2) MUTATED	16	60	24
DEL PEAK 39(17P11.2) WILD-TYPE	105	117	70

Figure S629. Get High-res Image Gene #88: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

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

Table S630. Gene #89: '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 S630. Get High-res Image Gene #89: '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 S631. Gene #89: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 40(17Q11.2) MUTATED	2	13	86	0	0
DEL PEAK 40(17Q11.2) WILD-TYPE	303	35	68	12	5

Figure S631. Get High-res Image Gene #89: '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 S632. Gene #89: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 40(17Q11.2) MUTATED	54	18	14
DEL PEAK 40(17Q11.2) WILD-TYPE	104	68	152

Figure S632. Get High-res Image Gene #89: '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 S633. Gene #89: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 40(17Q11.2) MUTATED	80	7	13
DEL PEAK 40(17Q11.2) WILD-TYPE	144	143	132

Figure S633. Get High-res Image Gene #89: '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 S634. Gene #89: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 40(17Q11.2) MUTATED	63	22	15
DEL PEAK 40(17Q11.2) WILD-TYPE	100	191	128

Figure S634. Get High-res Image Gene #89: '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 S635. Gene #89: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 40(17Q11.2) MUTATED	10	70	17
DEL PEAK 40(17Q11.2) WILD-TYPE	131	149	138

Figure S635. Get High-res Image Gene #89: '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 S636. Gene #89: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 40(17Q11.2) MUTATED	2	58	12	25
DEL PEAK 40(17Q11.2) WILD-TYPE	53	104	104	157

Figure S636. Get High-res Image Gene #89: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.19

Table S637. Gene #90: '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	7	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	14	10	12	10

Figure S637. Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S638. Gene #90: '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	6	0	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	13	3	7	7	16

Figure S638. Get High-res Image Gene #90: '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 S639. Gene #90: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 41(17Q21.31) MUTATED	1	12	87	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	304	36	67	12	5

Figure S639. Get High-res Image Gene #90: '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 S640. Gene #90: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 41(17Q21.31) MUTATED	57	18	13
DEL PEAK 41(17Q21.31) WILD-TYPE	101	68	153

Figure S640. Get High-res Image Gene #90: '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 S641. Gene #90: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 41(17Q21.31) MUTATED	79	6	14
DEL PEAK 41(17Q21.31) WILD-TYPE	145	144	131

Figure S641. Get High-res Image Gene #90: '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 S642. Gene #90: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 41(17Q21.31) MUTATED	63	21	15
DEL PEAK 41(17Q21.31) WILD-TYPE	100	192	128

Figure S642. Get High-res Image Gene #90: '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 S643. Gene #90: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 41(17Q21.31) MUTATED	11	68	17
DEL PEAK 41(17Q21.31) WILD-TYPE	130	151	138

Figure S643. Get High-res Image Gene #90: '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 S644. Gene #90: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 41(17Q21.31) MUTATED	1	57	13	25
DEL PEAK 41(17Q21.31) WILD-TYPE	54	105	103	157

Figure S644. Get High-res Image Gene #90: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

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

Table S645. Gene #91: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 42(18Q21.2) MUTATED	2	17	69	0	2
DEL PEAK 42(18Q21.2) WILD-TYPE	303	31	85	12	3

Figure S645. Get High-res Image Gene #91: '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 S646. Gene #91: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 42(18Q21.2) MUTATED	56	14	10
DEL PEAK 42(18Q21.2) WILD-TYPE	102	72	156

Figure S646. Get High-res Image Gene #91: '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 S647. Gene #91: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 42(18Q21.2) MUTATED	74	6	10
DEL PEAK 42(18Q21.2) WILD-TYPE	150	144	135

Figure S647. Get High-res Image Gene #91: '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 S648. Gene #91: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 42(18Q21.2) MUTATED	55	24	11
DEL PEAK 42(18Q21.2) WILD-TYPE	108	189	132

Figure S648. Get High-res Image Gene #91: '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 S649. Gene #91: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 42(18Q21.2) MUTATED	7	71	11
DEL PEAK 42(18Q21.2) WILD-TYPE	134	148	144

Figure S649. Get High-res Image Gene #91: '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 S650. Gene #91: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 42(18Q21.2) MUTATED	0	56	6	27
DEL PEAK 42(18Q21.2) WILD-TYPE	55	106	110	155

Figure S650. Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.18

Table S651. Gene #91: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 42(18Q21.2) MUTATED	12	50	17
DEL PEAK 42(18Q21.2) WILD-TYPE	109	127	77

Figure S651. Get High-res Image Gene #91: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'CN_CNMF'

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

Table S652. Gene #92: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 43(18Q23) MUTATED	2	18	74	1	1
DEL PEAK 43(18Q23) WILD-TYPE	303	30	80	11	4

Figure S652. Get High-res Image Gene #92: '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 S653. Gene #92: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 43(18Q23) MUTATED	60	14	10
DEL PEAK 43(18Q23) WILD-TYPE	98	72	156

Figure S653. Get High-res Image Gene #92: '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 S654. Gene #92: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 43(18Q23) MUTATED	80	6	10
DEL PEAK 43(18Q23) WILD-TYPE	144	144	135

Figure S654. Get High-res Image Gene #92: '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 S655. Gene #92: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 43(18Q23) MUTATED	62	23	11
DEL PEAK 43(18Q23) WILD-TYPE	101	190	132

Figure S655. Get High-res Image Gene #92: '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 S656. Gene #92: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 43(18Q23) MUTATED	9	72	13
DEL PEAK 43(18Q23) WILD-TYPE	132	147	142

Figure S656. Get High-res Image Gene #92: '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 S657. Gene #92: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 43(18Q23) MUTATED	1	63	7	23
DEL PEAK 43(18Q23) WILD-TYPE	54	99	109	159

Figure S657. Get High-res Image Gene #92: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

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

Table S658. Gene #93: '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 S658. Get High-res Image Gene #93: '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 S659. Gene #93: '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 S659. Get High-res Image Gene #93: '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 S660. Gene #93: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 44(19P13.3) MUTATED	1	14	131	0	1
DEL PEAK 44(19P13.3) WILD-TYPE	304	34	23	12	4

Figure S660. Get High-res Image Gene #93: '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 S661. Gene #93: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 44(19P13.3) MUTATED	101	23	5
DEL PEAK 44(19P13.3) WILD-TYPE	57	63	161

Figure S661. Get High-res Image Gene #93: '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 = 0.017

Table S662. Gene #93: '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 S662. Get High-res Image Gene #93: '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 S663. Gene #93: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 44(19P13.3) MUTATED	133	4	9
DEL PEAK 44(19P13.3) WILD-TYPE	91	146	136

Figure S663. Get High-res Image Gene #93: '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 S664. Gene #93: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 44(19P13.3) MUTATED	115	23	8
DEL PEAK 44(19P13.3) WILD-TYPE	48	190	135

Figure S664. Get High-res Image Gene #93: '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 S665. Gene #93: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 44(19P13.3) MUTATED	8	123	11
DEL PEAK 44(19P13.3) WILD-TYPE	133	96	144

Figure S665. Get High-res Image Gene #93: '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 S666. Gene #93: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 44(19P13.3) MUTATED	1	108	8	25
DEL PEAK 44(19P13.3) WILD-TYPE	54	54	108	157

Figure S666. Get High-res Image Gene #93: '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 S667. Gene #93: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 44(19P13.3) MUTATED	13	81	32
DEL PEAK 44(19P13.3) WILD-TYPE	108	96	62

Figure S667. Get High-res Image Gene #93: '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 S668. Gene #93: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 44(19P13.3) MUTATED	76	13	37
DEL PEAK 44(19P13.3) WILD-TYPE	95	95	76

Figure S668. Get High-res Image Gene #93: '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 S669. Gene #94: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 45(19P12) MUTATED	1	13	42	0	0
DEL PEAK 45(19P12) WILD-TYPE	304	35	112	12	5

Figure S669. Get High-res Image Gene #94: '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 S670. Gene #94: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 45(19P12) MUTATED	36	10	4
DEL PEAK 45(19P12) WILD-TYPE	122	76	162

Figure S670. Get High-res Image Gene #94: '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 S671. Gene #94: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 45(19P12) MUTATED	45	5	6
DEL PEAK 45(19P12) WILD-TYPE	179	145	139

Figure S671. Get High-res Image Gene #94: '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 S672. Gene #94: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 45(19P12) MUTATED	38	13	5
DEL PEAK 45(19P12) WILD-TYPE	125	200	138

Figure S672. Get High-res Image Gene #94: '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 S673. Gene #94: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 45(19P12) MUTATED	8	42	5
DEL PEAK 45(19P12) WILD-TYPE	133	177	150

Figure S673. Get High-res Image Gene #94: '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 S674. Gene #94: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 45(19P12) MUTATED	1	36	4	14
DEL PEAK 45(19P12) WILD-TYPE	54	126	112	168

Figure S674. Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.16

Table S675. Gene #94: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 45(19P12) MUTATED	35	6	9
DEL PEAK 45(19P12) WILD-TYPE	136	102	104

Figure S675. Get High-res Image Gene #94: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

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

Table S676. Gene #95: '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 S676. Get High-res Image Gene #95: '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 S677. Gene #95: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 46(19Q13.43) MUTATED	2	9	53	0	0
DEL PEAK 46(19Q13.43) WILD-TYPE	303	39	101	12	5

Figure S677. Get High-res Image Gene #95: '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 S678. Gene #95: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 46(19Q13.43) MUTATED	40	11	2
DEL PEAK 46(19Q13.43) WILD-TYPE	118	75	164

Figure S678. Get High-res Image Gene #95: '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 S679. Gene #95: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 46(19Q13.43) MUTATED	56	4	3
DEL PEAK 46(19Q13.43) WILD-TYPE	168	146	142

Figure S679. Get High-res Image Gene #95: '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 S680. Gene #95: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 46(19Q13.43) MUTATED	49	11	3
DEL PEAK 46(19Q13.43) WILD-TYPE	114	202	140

Figure S680. Get High-res Image Gene #95: '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 S681. Gene #95: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 46(19Q13.43) MUTATED	3	52	5
DEL PEAK 46(19Q13.43) WILD-TYPE	138	167	150

Figure S681. Get High-res Image Gene #95: '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 S682. Gene #95: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 46(19Q13.43) MUTATED	0	46	2	12
DEL PEAK 46(19Q13.43) WILD-TYPE	55	116	114	170

Figure S682. Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.033

Table S683. Gene #95: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 46(19Q13.43) MUTATED	4	34	16
DEL PEAK 46(19Q13.43) WILD-TYPE	117	143	78

Figure S683. Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.048

Table S684. Gene #95: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	171	108	113
DEL PEAK 46(19Q13.43) MUTATED	30	3	21
DEL PEAK 46(19Q13.43) WILD-TYPE	141	105	92

Figure S684. Get High-res Image Gene #95: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

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

Table S685. Gene #96: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 47(20P12.1) MUTATED	6	6	21	1	0
DEL PEAK 47(20P12.1) WILD-TYPE	299	42	133	11	5

Figure S685. Get High-res Image Gene #96: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.1' versus 'CN_CNMF'

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

Table S686. Gene #97: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 48(22Q11.1) MUTATED	3	15	65	0	1
DEL PEAK 48(22Q11.1) WILD-TYPE	302	33	89	12	4

Figure S686. Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

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

Table S687. Gene #97: 'del_22q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 48(22Q11.1) MUTATED	45	15	14
DEL PEAK 48(22Q11.1) WILD-TYPE	113	71	152

Figure S687. Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MRNASEQ_CNMF'

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

Table S688. Gene #97: 'del_22q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 48(22Q11.1) MUTATED	63	6	15
DEL PEAK 48(22Q11.1) WILD-TYPE	161	144	130

Figure S688. Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S689. Gene #97: 'del_22q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 48(22Q11.1) MUTATED	47	22	15
DEL PEAK 48(22Q11.1) WILD-TYPE	116	191	128

Figure S689. Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

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

Table S690. Gene #97: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 48(22Q11.1) MUTATED	10	55	17
DEL PEAK 48(22Q11.1) WILD-TYPE	131	164	138

Figure S690. Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S691. Gene #97: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 48(22Q11.1) MUTATED	2	46	12	22
DEL PEAK 48(22Q11.1) WILD-TYPE	53	116	104	160

Figure S691. Get High-res Image Gene #97: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MRNA_CNMF'

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

Table S692. Gene #98: 'del_22q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 49(22Q13.31) MUTATED	0	10	0	0
DEL PEAK 49(22Q13.31) WILD-TYPE	14	7	12	10

Figure S692. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.31' versus 'MRNA_CHIERARCHICAL'

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

Table S693. Gene #98: 'del_22q13.31' 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 49(22Q13.31) MUTATED	2	8	0	0	0
DEL PEAK 49(22Q13.31) WILD-TYPE	12	1	7	7	16

Figure S693. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

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

Table S694. Gene #98: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 49(22Q13.31) MUTATED	4	15	111	0	2
DEL PEAK 49(22Q13.31) WILD-TYPE	301	33	43	12	3

Figure S694. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

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

Table S695. Gene #98: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 49(22Q13.31) MUTATED	79	21	15
DEL PEAK 49(22Q13.31) WILD-TYPE	79	65	151

Figure S695. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

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

Table S696. Gene #98: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 49(22Q13.31) MUTATED	107	8	16
DEL PEAK 49(22Q13.31) WILD-TYPE	117	142	129

Figure S696. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S697. Gene #98: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 49(22Q13.31) MUTATED	88	26	17
DEL PEAK 49(22Q13.31) WILD-TYPE	75	187	126

Figure S697. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

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

Table S698. Gene #98: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 49(22Q13.31) MUTATED	11	97	19
DEL PEAK 49(22Q13.31) WILD-TYPE	130	122	136

Figure S698. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S699. Gene #98: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 49(22Q13.31) MUTATED	1	83	12	31
DEL PEAK 49(22Q13.31) WILD-TYPE	54	79	104	151

Figure S699. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.13

Table S700. Gene #98: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	121	177	94
DEL PEAK 49(22Q13.31) MUTATED	19	66	26
DEL PEAK 49(22Q13.31) WILD-TYPE	102	111	68

Figure S700. Get High-res Image Gene #98: 'del_22q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'CN_CNMF'

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

Table S701. Gene #99: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	305	48	154	12	5
DEL PEAK 50(XP21.1) MUTATED	2	10	72	0	0
DEL PEAK 50(XP21.1) WILD-TYPE	303	38	82	12	5

Figure S701. Get High-res Image Gene #99: '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 S702. Gene #99: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	158	86	166
DEL PEAK 50(XP21.1) MUTATED	50	12	9
DEL PEAK 50(XP21.1) WILD-TYPE	108	74	157

Figure S702. Get High-res Image Gene #99: '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 S703. Gene #99: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	150	145
DEL PEAK 50(XP21.1) MUTATED	72	5	6
DEL PEAK 50(XP21.1) WILD-TYPE	152	145	139

Figure S703. Get High-res Image Gene #99: '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 S704. Gene #99: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	213	143
DEL PEAK 50(XP21.1) MUTATED	61	17	5
DEL PEAK 50(XP21.1) WILD-TYPE	102	196	138

Figure S704. Get High-res Image Gene #99: '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 S705. Gene #99: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	141	219	155
DEL PEAK 50(XP21.1) MUTATED	8	64	9
DEL PEAK 50(XP21.1) WILD-TYPE	133	155	146

Figure S705. Get High-res Image Gene #99: '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 S706. Gene #99: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	55	162	116	182
DEL PEAK 50(XP21.1) MUTATED	1	57	5	18
DEL PEAK 50(XP21.1) WILD-TYPE	54	105	111	164

Figure S706. Get High-res Image Gene #99: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = UCEC-TP.transferedmergedcluster.txt
Number of patients = 524
Number of significantly focal cnvs = 99
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)

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