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 79 focal events and 14 molecular subtypes across 1090 patients, 667 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_1q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_3p25.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_3q26.33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_4q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q32.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_10p15.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q24.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.32 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'MIR_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_14q32.33 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_17p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'RPPA_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_17q25.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_19p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p32.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p22.1 cnv correlated to 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q42.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_2q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', and 'METHLYATION_CNMF'.
del_2q37.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_3p21.31 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3q13.31 cnv correlated to 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3q29 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5p15.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_5q34 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6q22.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8q24.3 cnv correlated to 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p11.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_11p15.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_12q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_12q15 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_14q13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q31.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q14 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_16p12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', and 'METHLYATION_CNMF'.
del_19q13.41 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.43 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MIR_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_xq21.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'MIR_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 focal events and 14 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 667 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	MIR CNMF	MIR 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	Fisher's exact test	Fisher's exact test
amp 7p11 2	635 (58%)	455	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0001 (0.000318)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00032 (0.000917)	1e-05 (3.8e-05)	4e-05 (0.000137)	1e-05 (3.8e-05)
amp 7q11 21	581 (53%)	509	1e-05 (3.8e-05)	1e-05 (3.8e-05)	3e-05 (0.000107)	4e-05 (0.000137)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00112 (0.00287)	0.00095 (0.00247)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00447 (0.00985)	1e-05 (3.8e-05)	0.00023 (0.000671)	1e-05 (3.8e-05)
amp 7q31 2	646 (59%)	444	0.00114 (0.00291)	1e-05 (3.8e-05)	0.0137 (0.0263)	0.00906 (0.0182)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00858 (0.0172)	0.025 (0.045)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0102 (0.0203)	1e-05 (3.8e-05)	0.00859 (0.0172)	1e-05 (3.8e-05)
del 10p15 3	553 (51%)	537	2e-05 (7.25e-05)	1e-05 (3.8e-05)	0.00822 (0.0166)	0.00355 (0.00798)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00039 (0.00111)	0.00061 (0.00167)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	9e-05 (0.000292)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 10p13	553 (51%)	537	2e-05 (7.25e-05)	1e-05 (3.8e-05)	0.00248 (0.00584)	0.00133 (0.00334)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	5e-05 (0.000169)	7e-05 (0.000229)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	4e-05 (0.000137)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 10p11 23	558 (51%)	532	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00012 (0.000374)	3e-05 (0.000107)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00062 (0.00168)	0.00024 (0.000695)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	4e-05 (0.000137)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 10q23 31	628 (58%)	462	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0121 (0.0235)	0.00299 (0.0069)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	4e-05 (0.000137)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 10q26 3	665 (61%)	425	1e-05 (3.8e-05)	2e-05 (7.25e-05)	0.0425 (0.0718)	0.00155 (0.0038)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	2e-05 (7.25e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
amp 7q21 2	636 (58%)	454	4e-05 (0.000137)	1e-05 (3.8e-05)	0.05 (0.0828)	0.0001 (0.000318)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00488 (0.0106)	0.0122 (0.0239)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00406 (0.00898)	1e-05 (3.8e-05)	0.00082 (0.00217)	1e-05 (3.8e-05)
amp 19q12	247 (23%)	843	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.284 (0.354)	0.00465 (0.0101)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0235 (0.0426)	0.00083 (0.0022)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00018 (0.000534)	1e-05 (3.8e-05)	3e-05 (0.000107)	1e-05 (3.8e-05)
amp 19q13 2	231 (21%)	859	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.221 (0.287)	0.0068 (0.014)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00464 (0.0101)	0.00118 (0.00299)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00016 (0.000483)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 19q13 41	366 (34%)	724	0.00453 (0.00996)	5e-05 (0.000169)	0.0761 (0.118)	0.0443 (0.0744)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0433 (0.073)	0.00132 (0.00332)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
amp 7q32 3	659 (60%)	431	0.00022 (0.000644)	6e-05 (0.000199)	0.0715 (0.112)	0.00471 (0.0103)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00531 (0.0114)	0.0159 (0.0301)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0546 (0.089)	1e-05 (3.8e-05)	0.022 (0.0402)	1e-05 (3.8e-05)
amp 19p13 3	375 (34%)	715	1e-05 (3.8e-05)	4e-05 (0.000137)	0.0254 (0.0455)	0.00245 (0.00578)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0939 (0.141)	0.0265 (0.0472)	0.00179 (0.00435)	1e-05 (3.8e-05)	0.00011 (0.000347)	0.156 (0.217)	0.0449 (0.0753)	0.00078 (0.00207)
amp 19p13 2	371 (34%)	719	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.148 (0.207)	0.00135 (0.00337)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0177 (0.0332)	0.00655 (0.0135)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00024 (0.000695)	0.141 (0.199)	0.0407 (0.0695)	0.00056 (0.00154)
del 9p21 3	593 (54%)	497	2e-05 (7.25e-05)	2e-05 (7.25e-05)	0.568 (0.63)	0.0174 (0.0328)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.266 (0.334)	1e-05 (3.8e-05)	0.0012 (0.00304)	1e-05 (3.8e-05)
del 19q13 43	354 (32%)	736	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00094 (0.00246)	0.0567 (0.0914)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.13 (0.185)	0.00792 (0.016)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
amp 3q26 33	132 (12%)	958	0.00781 (0.0158)	0.21 (0.274)	0.45 (0.521)	0.0572 (0.092)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00985 (0.0196)	0.00691 (0.0142)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00348 (0.00789)	0.0186 (0.0348)	0.0215 (0.0397)	0.00202 (0.00484)
del 1p22 1	234 (21%)	856	0.977 (0.985)	0.553 (0.616)	0.813 (0.854)	0.0049 (0.0106)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0222 (0.0404)	6e-05 (0.000199)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 22q13 32	289 (27%)	801	0.719 (0.768)	0.972 (0.982)	0.0396 (0.0679)	0.414 (0.486)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00011 (0.000347)	0.00217 (0.00516)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0216 (0.0399)	1e-05 (3.8e-05)	0.00051 (0.00141)	0.00011 (0.000347)
amp 1p36 21	104 (10%)	986	0.588 (0.647)	0.428 (0.5)	0.404 (0.477)	0.117 (0.168)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0222 (0.0405)	0.0208 (0.0386)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.013 (0.0252)	1e-05 (3.8e-05)	0.0338 (0.0588)	0.00076 (0.00203)
del 1p36 32	318 (29%)	772	0.836 (0.873)	0.703 (0.752)	0.701 (0.751)	0.254 (0.322)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0103 (0.0204)	0.00051 (0.00141)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 1p32 3	257 (24%)	833	0.243 (0.312)	0.367 (0.441)	0.83 (0.868)	0.158 (0.218)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00229 (0.00544)	3e-05 (0.000107)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 2q37 1	121 (11%)	969	0.1 (0.149)	0.00587 (0.0123)	0.315 (0.387)	0.823 (0.862)	0.00491 (0.0106)	1e-05 (3.8e-05)	0.0119 (0.0233)	0.0058 (0.0122)	0.0239 (0.0431)	1e-05 (3.8e-05)	0.00118 (0.00299)	0.022 (0.0402)	0.00107 (0.00275)	0.143 (0.201)
del 4q34 3	231 (21%)	859	0.00523 (0.0112)	0.00029 (0.000835)	0.0754 (0.118)	0.0963 (0.145)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.202 (0.268)	0.818 (0.859)	0.00191 (0.0046)	0.00022 (0.000644)	0.0304 (0.0535)	0.0378 (0.0652)	0.00103 (0.00266)	0.00545 (0.0116)
del 11p15 1	176 (16%)	914	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.808 (0.85)	0.0772 (0.119)	0.00262 (0.00613)	1e-05 (3.8e-05)	0.0427 (0.0722)	0.545 (0.612)	0.00111 (0.00285)	1e-05 (3.8e-05)	2e-05 (7.25e-05)	0.0001 (0.000318)	0.874 (0.901)	0.0335 (0.0583)
del 11p11 2	159 (15%)	931	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.502 (0.569)	0.0191 (0.0356)	0.00012 (0.000374)	1e-05 (3.8e-05)	0.0977 (0.146)	0.467 (0.538)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00046 (0.00128)	1e-05 (3.8e-05)	0.385 (0.457)	0.00043 (0.00121)
del 14q24 2	292 (27%)	798	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0579 (0.0928)	0.156 (0.216)	0.00576 (0.0122)	0.159 (0.218)	0.0252 (0.0452)	0.204 (0.268)	9e-05 (0.000292)	0.00016 (0.000483)	0.0004 (0.00113)	0.00511 (0.011)	0.0042 (0.00927)	0.00143 (0.00352)
del 14q31 3	275 (25%)	815	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.343 (0.416)	0.164 (0.225)	0.00553 (0.0117)	0.0997 (0.149)	0.0334 (0.0581)	0.353 (0.426)	0.00031 (0.000891)	0.00033 (0.000941)	0.00097 (0.00252)	0.00794 (0.016)	0.00716 (0.0147)	0.00344 (0.00781)
del 17q11 2	93 (9%)	997	2e-05 (7.25e-05)	4e-05 (0.000137)	0.00262 (0.00613)	0.0109 (0.0216)	1e-05 (3.8e-05)	0.00021 (0.000618)	0.0627 (0.0995)	0.0013 (0.00328)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.172 (0.233)	0.136 (0.192)	0.778 (0.822)	0.00613 (0.0127)
amp 4q12	138 (13%)	952	0.00065 (0.00176)	0.00323 (0.00738)	0.535 (0.603)	0.472 (0.543)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.339 (0.412)	0.0556 (0.09)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00302 (0.00696)	0.00016 (0.000483)	0.943 (0.96)	0.00393 (0.00873)
amp 8q24 21	169 (16%)	921	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0161 (0.0304)	0.236 (0.304)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.669 (0.722)	0.434 (0.506)	0.00061 (0.00167)	1e-05 (3.8e-05)	0.076 (0.118)	0.00089 (0.00234)	0.111 (0.162)	6e-05 (0.000199)
amp 10p15 1	88 (8%)	1002	0.00015 (0.000458)	2e-05 (7.25e-05)	0.00545 (0.0116)	0.0578 (0.0928)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.425 (0.498)	0.146 (0.204)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00045 (0.00126)	0.219 (0.285)	0.38 (0.452)	0.00088 (0.00232)
del 1p36 23	348 (32%)	742	0.0702 (0.11)	0.183 (0.247)	0.569 (0.63)	0.554 (0.617)	0.00017 (0.000507)	1e-05 (3.8e-05)	0.104 (0.153)	0.011 (0.0216)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	1e-05 (3.8e-05)
del 6q22 31	236 (22%)	854	0.633 (0.69)	0.99 (0.996)	0.294 (0.364)	0.285 (0.354)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00353 (0.00795)	0.00188 (0.00454)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00067 (0.00181)	0.12 (0.172)	0.00596 (0.0125)	2e-05 (7.25e-05)
del 6q26	261 (24%)	829	0.743 (0.789)	0.756 (0.801)	0.477 (0.547)	0.548 (0.614)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.00014 (0.000434)	6e-05 (0.000199)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	4e-05 (0.000137)	0.16 (0.219)	0.00378 (0.00843)	1e-05 (3.8e-05)
del 14q13 1	246 (23%)	844	2e-05 (7.25e-05)	0.00015 (0.000458)	0.614 (0.671)	0.663 (0.718)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0853 (0.131)	0.313 (0.385)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0628 (0.0995)	0.00016 (0.000483)	0.00285 (0.00664)	2e-05 (7.25e-05)
amp 1q22	144 (13%)	946	0.0132 (0.0255)	0.0257 (0.046)	0.0416 (0.0708)	0.379 (0.452)	1e-05 (3.8e-05)	0.00019 (0.000562)	0.0367 (0.0635)	0.203 (0.268)	1e-05 (3.8e-05)	7e-05 (0.000229)	0.569 (0.63)	0.0903 (0.137)	0.155 (0.215)	0.313 (0.385)
amp 12q14 1	171 (16%)	919	0.0672 (0.106)	0.147 (0.206)	0.1 (0.149)	0.0881 (0.134)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.121 (0.173)	0.925 (0.944)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0028 (0.00653)	1e-05 (3.8e-05)	0.0419 (0.0711)	1e-05 (3.8e-05)
del 5q34	133 (12%)	957	1e-05 (3.8e-05)	1e-05 (3.8e-05)	6e-05 (0.000199)	0.00579 (0.0122)	0.00012 (0.000374)	1e-05 (3.8e-05)	0.264 (0.333)	0.0882 (0.134)	0.0542 (0.0887)	1e-05 (3.8e-05)	0.00012 (0.000374)	0.056 (0.0906)	0.571 (0.632)	0.392 (0.464)
del 8q24 3	78 (7%)	1012	0.178 (0.24)	0.868 (0.898)	0.00339 (0.00773)	0.464 (0.536)	0.0001 (0.000318)	1e-05 (3.8e-05)	0.109 (0.16)	0.108 (0.158)	0.0238 (0.0431)	0.00361 (0.0081)	0.00496 (0.0107)	0.00137 (0.00341)	0.193 (0.257)	0.0225 (0.0409)
del 11p15 5	234 (21%)	856	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.162 (0.222)	0.00161 (0.00394)	0.00077 (0.00205)	1e-05 (3.8e-05)	0.0962 (0.145)	0.905 (0.928)	0.227 (0.294)	1e-05 (3.8e-05)	5e-05 (0.000169)	0.0123 (0.0239)	1 (1.00)	0.901 (0.924)
del 13q14 2	383 (35%)	707	1e-05 (3.8e-05)	4e-05 (0.000137)	0.354 (0.427)	0.145 (0.203)	1e-05 (3.8e-05)	0.00017 (0.000507)	0.2 (0.265)	0.582 (0.641)	5e-05 (0.000169)	1e-05 (3.8e-05)	0.0175 (0.0329)	0.00589 (0.0123)	0.474 (0.544)	0.413 (0.486)
del 13q22 1	367 (34%)	723	1e-05 (3.8e-05)	0.00015 (0.000458)	0.51 (0.577)	0.338 (0.412)	1e-05 (3.8e-05)	0.00177 (0.00432)	0.13 (0.186)	0.916 (0.937)	0.00013 (0.000404)	2e-05 (7.25e-05)	0.0159 (0.0301)	0.00178 (0.00434)	0.359 (0.431)	0.207 (0.271)
del 15q14	214 (20%)	876	2e-05 (7.25e-05)	1e-05 (3.8e-05)	0.00071 (0.00191)	0.00015 (0.000458)	7e-05 (0.000229)	0.00192 (0.00461)	0.196 (0.261)	0.0583 (0.0934)	4e-05 (0.000137)	0.00046 (0.00128)	0.473 (0.544)	0.758 (0.802)	0.133 (0.189)	0.0594 (0.0948)
del 16q23 1	129 (12%)	961	0.0148 (0.0282)	0.488 (0.557)	0.874 (0.901)	0.536 (0.603)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0688 (0.108)	0.00052 (0.00144)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.248 (0.316)	0.0144 (0.0276)	0.197 (0.262)	0.0324 (0.0567)
del 17p13 1	116 (11%)	974	0.00024 (0.000695)	0.00138 (0.00342)	0.628 (0.685)	0.898 (0.922)	1e-05 (3.8e-05)	0.00045 (0.00126)	0.193 (0.258)	0.0629 (0.0995)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.186 (0.25)	0.00363 (0.00813)	0.613 (0.671)	0.0441 (0.0742)
amp 1q32 1	205 (19%)	885	0.82 (0.859)	0.0617 (0.0984)	0.333 (0.407)	0.149 (0.207)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.0973 (0.146)	0.229 (0.296)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.342 (0.415)	1e-05 (3.8e-05)	0.00074 (0.00198)	1e-05 (3.8e-05)
amp 5p15 33	76 (7%)	1014	0.0344 (0.0596)	0.0854 (0.131)	0.104 (0.152)	0.233 (0.301)	3e-05 (0.000107)	0.0093 (0.0186)	0.427 (0.5)	0.198 (0.263)	6e-05 (0.000199)	0.00033 (0.000941)	0.143 (0.201)	0.0032 (0.00733)	0.169 (0.23)	0.0374 (0.0645)
amp 9q34 3	140 (13%)	950	0.00652 (0.0135)	0.00608 (0.0127)	0.234 (0.301)	0.0563 (0.0909)	0.00186 (0.0045)	0.0397 (0.0679)	0.0305 (0.0535)	0.985 (0.992)	0.0108 (0.0213)	0.0177 (0.0331)	0.201 (0.266)	0.0858 (0.131)	0.282 (0.353)	0.285 (0.354)
amp 11q24 1	112 (10%)	978	0.00403 (0.00893)	0.00771 (0.0157)	0.0912 (0.138)	0.0679 (0.107)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.209 (0.273)	0.0866 (0.132)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.761 (0.805)	0.114 (0.165)	0.855 (0.888)	0.0437 (0.0736)
amp 12p13 32	152 (14%)	938	0.664 (0.718)	0.384 (0.457)	0.343 (0.416)	0.431 (0.503)	0.865 (0.895)	1e-05 (3.8e-05)	0.00245 (0.00578)	0.012 (0.0235)	0.00351 (0.00792)	1e-05 (3.8e-05)	0.00319 (0.00732)	0.00341 (0.00776)	0.0516 (0.0849)	0.0762 (0.118)
del 5p15 33	107 (10%)	983	1e-05 (3.8e-05)	3e-05 (0.000107)	0.00142 (0.00351)	0.0541 (0.0886)	0.00648 (0.0134)	1e-05 (3.8e-05)	0.143 (0.201)	0.637 (0.694)	0.104 (0.153)	0.00296 (0.00685)	0.00207 (0.00494)	0.207 (0.271)	0.947 (0.962)	0.442 (0.513)
del 16p12 2	114 (10%)	976	0.247 (0.315)	0.234 (0.301)	0.397 (0.47)	0.872 (0.901)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.24 (0.308)	0.0159 (0.0301)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.656 (0.711)	0.0217 (0.04)	0.962 (0.973)	0.00549 (0.0117)
del xp22 2	228 (21%)	862	0.00611 (0.0127)	0.00145 (0.00356)	0.111 (0.162)	0.169 (0.23)	0.0619 (0.0985)	0.00371 (0.00829)	0.00293 (0.00681)	0.0212 (0.0393)	0.051 (0.0842)	0.0171 (0.0324)	0.0308 (0.0541)	0.37 (0.444)	0.0556 (0.09)	0.0756 (0.118)
del xq21 1	184 (17%)	906	0.0622 (0.0988)	0.00089 (0.00234)	0.038 (0.0653)	0.102 (0.15)	0.492 (0.56)	0.0106 (0.021)	0.00062 (0.00168)	0.0316 (0.0554)	0.00121 (0.00306)	0.258 (0.327)	0.00103 (0.00266)	0.358 (0.431)	0.119 (0.171)	0.159 (0.218)
amp 1q44	129 (12%)	961	0.145 (0.203)	0.625 (0.682)	0.604 (0.663)	0.309 (0.381)	1e-05 (3.8e-05)	7e-05 (0.000229)	0.0262 (0.0468)	0.138 (0.195)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.434 (0.506)	0.0219 (0.0402)	0.0553 (0.0898)	0.0802 (0.124)
amp xp11 21	104 (10%)	986	0.24 (0.308)	0.782 (0.825)	0.578 (0.637)	0.972 (0.982)	5e-05 (0.000169)	1e-05 (3.8e-05)	0.215 (0.281)	0.0518 (0.0851)	0.00306 (0.00704)	1e-05 (3.8e-05)	8e-05 (0.000261)	0.268 (0.337)	0.189 (0.253)	0.0035 (0.00792)
del 3p21 31	108 (10%)	982	0.189 (0.253)	0.168 (0.23)	0.476 (0.546)	0.293 (0.363)	0.102 (0.151)	0.00095 (0.00247)	0.00093 (0.00244)	0.0379 (0.0652)	0.0876 (0.133)	0.0251 (0.0451)	0.00134 (0.00335)	0.00249 (0.00585)	0.721 (0.769)	0.0667 (0.105)
del 8p23 2	88 (8%)	1002	0.375 (0.449)	0.245 (0.314)	0.18 (0.242)	0.274 (0.344)	4e-05 (0.000137)	1e-05 (3.8e-05)	0.157 (0.217)	0.214 (0.279)	0.00017 (0.000507)	0.00026 (0.000751)	0.113 (0.164)	0.00765 (0.0156)	1 (1.00)	0.00138 (0.00342)
del 12q12	147 (13%)	943	0.0134 (0.0259)	0.00057 (0.00156)	0.27 (0.338)	0.0842 (0.129)	0.00515 (0.0111)	1e-05 (3.8e-05)	0.989 (0.995)	0.945 (0.961)	0.863 (0.894)	0.0001 (0.000318)	0.00707 (0.0145)	0.467 (0.538)	0.85 (0.885)	0.961 (0.973)
del 12q15	142 (13%)	948	0.00017 (0.000507)	0.00212 (0.00505)	0.487 (0.556)	0.423 (0.496)	0.0414 (0.0706)	1e-05 (3.8e-05)	0.752 (0.797)	0.917 (0.937)	0.678 (0.73)	1e-05 (3.8e-05)	0.00107 (0.00275)	0.313 (0.385)	0.928 (0.946)	0.941 (0.959)
amp 2p24 3	72 (7%)	1018	0.1 (0.149)	0.0177 (0.0331)	0.431 (0.503)	0.979 (0.987)	0.0299 (0.0527)	0.102 (0.151)	0.0661 (0.104)	0.499 (0.568)	0.00551 (0.0117)	0.00774 (0.0157)	0.545 (0.612)	0.0289 (0.0513)	0.615 (0.672)	0.122 (0.175)
amp 3p25 3	85 (8%)	1005	0.00047 (0.00131)	0.0146 (0.0278)	0.597 (0.657)	0.0512 (0.0844)	0.0546 (0.089)	0.0114 (0.0224)	0.0417 (0.0709)	0.136 (0.192)	0.0995 (0.148)	0.0229 (0.0415)	0.441 (0.512)	0.668 (0.721)	1 (1.00)	0.347 (0.419)
amp 17p13 2	74 (7%)	1016	0.00073 (0.00196)	0.0138 (0.0265)	0.0488 (0.0812)	0.112 (0.163)	0.0775 (0.12)	0.0972 (0.146)	0.00609 (0.0127)	0.206 (0.271)	0.535 (0.603)	0.854 (0.888)	0.248 (0.316)	0.674 (0.725)	0.033 (0.0576)	0.186 (0.249)
del 1q42 11	80 (7%)	1010	0.219 (0.285)	0.825 (0.863)	0.514 (0.581)	0.284 (0.354)	0.00958 (0.0191)	0.00018 (0.000534)	0.223 (0.29)	0.0717 (0.112)	0.166 (0.227)	0.0292 (0.0515)	0.0125 (0.0242)	0.113 (0.164)	0.639 (0.695)	0.0281 (0.0499)
del 6p25 3	138 (13%)	952	0.101 (0.15)	0.0901 (0.137)	0.376 (0.45)	0.889 (0.914)	0.0213 (0.0394)	0.00781 (0.0158)	0.164 (0.225)	0.0136 (0.0263)	0.00192 (0.00461)	0.00143 (0.00352)	0.413 (0.486)	0.252 (0.32)	0.145 (0.203)	0.0863 (0.132)
del 12p13 1	110 (10%)	980	0.0493 (0.0817)	0.0138 (0.0264)	0.254 (0.322)	0.232 (0.299)	0.0971 (0.146)	0.00721 (0.0147)	0.812 (0.853)	0.408 (0.481)	0.113 (0.164)	0.00182 (0.00441)	0.0571 (0.0919)	0.0457 (0.0765)	0.955 (0.969)	0.251 (0.319)
amp 4p16 3	70 (6%)	1020	0.309 (0.381)	0.724 (0.773)	0.859 (0.89)	0.084 (0.129)	0.00066 (0.00178)	0.0038 (0.00846)	0.458 (0.53)	0.0594 (0.0948)	0.0001 (0.000318)	0.0002 (0.00059)	0.119 (0.171)	0.337 (0.411)	0.609 (0.668)	0.259 (0.327)
amp 12q15	111 (10%)	979	0.73 (0.777)	0.316 (0.387)	0.707 (0.756)	0.279 (0.349)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.142 (0.2)	0.695 (0.746)	1e-05 (3.8e-05)	1e-05 (3.8e-05)	0.379 (0.452)	0.0552 (0.0898)	0.205 (0.269)	0.0543 (0.0887)
amp 17q25 1	128 (12%)	962	0.014 (0.0269)	0.256 (0.324)	0.283 (0.354)	0.727 (0.774)	0.0001 (0.000318)	0.229 (0.296)	0.185 (0.249)	0.645 (0.7)	0.0117 (0.023)	0.0346 (0.0599)	0.15 (0.209)	0.564 (0.626)	0.188 (0.252)	0.562 (0.625)
del 1q44	71 (7%)	1019	0.338 (0.412)	0.26 (0.328)	0.839 (0.875)	1 (1.00)	0.172 (0.233)	0.00015 (0.000458)	0.2 (0.265)	0.0269 (0.0479)	0.113 (0.164)	0.00454 (0.00996)	0.048 (0.0799)	0.55 (0.615)	0.435 (0.506)	0.163 (0.223)
del 2q22 1	68 (6%)	1022	0.00542 (0.0116)	0.029 (0.0513)	0.386 (0.458)	0.552 (0.616)	0.0386 (0.0663)	0.0458 (0.0765)	0.0872 (0.133)	0.542 (0.609)	0.119 (0.171)	0.0745 (0.116)	0.107 (0.157)	0.801 (0.844)	0.842 (0.877)	0.289 (0.358)
del 3q13 31	95 (9%)	995	0.573 (0.634)	0.346 (0.419)	0.609 (0.668)	0.514 (0.581)	0.85 (0.885)	0.00295 (0.00684)	0.134 (0.191)	0.0198 (0.0367)	0.387 (0.458)	0.0462 (0.0771)	0.157 (0.218)	0.00055 (0.00152)	0.574 (0.634)	0.115 (0.166)
amp 13q34	54 (5%)	1036	0.261 (0.328)	0.204 (0.268)	0.0292 (0.0515)	0.481 (0.55)	0.5 (0.568)	0.00118 (0.00299)	0.0636 (0.101)	0.46 (0.532)	0.135 (0.191)	0.027 (0.0481)	0.296 (0.366)	0.69 (0.741)	0.961 (0.973)	0.051 (0.0842)
amp 14q32 33	44 (4%)	1046	0.187 (0.251)	0.657 (0.712)	0.0905 (0.137)	0.921 (0.94)	0.00034 (0.000967)	0.501 (0.569)	0.335 (0.409)	0.316 (0.388)	0.0218 (0.0401)	0.00925 (0.0185)	1 (1.00)	0.523 (0.59)	0.743 (0.789)	0.562 (0.625)
del 3q29	107 (10%)	983	0.169 (0.23)	0.173 (0.234)	0.551 (0.616)	0.856 (0.888)	1 (1.00)	0.00239 (0.00566)	0.329 (0.403)	0.67 (0.722)	0.053 (0.0869)	0.00503 (0.0108)	0.236 (0.304)	0.0424 (0.0718)	0.888 (0.914)	0.406 (0.479)
del 18q23	151 (14%)	939	0.0489 (0.0813)	0.0193 (0.0359)	0.739 (0.786)	0.504 (0.571)	0.481 (0.55)	0.00465 (0.0101)	0.116 (0.168)	0.418 (0.491)	0.912 (0.934)	0.65 (0.705)	0.31 (0.383)	0.883 (0.91)	0.684 (0.736)	0.379 (0.452)
amp 11p13	60 (6%)	1030	0.785 (0.828)	0.348 (0.421)	0.549 (0.614)	0.248 (0.316)	0.479 (0.549)	0.00017 (0.000507)	0.172 (0.233)	0.158 (0.218)	0.459 (0.531)	0.1 (0.149)	0.0772 (0.119)	0.117 (0.168)	0.363 (0.436)	0.0225 (0.0409)

'amp_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S1. Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 1(1P36.21) MUTATED	91	7	6
AMP PEAK 1(1P36.21) WILD-TYPE	442	535	9

Figure S1. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S2. Gene #1: 'amp_1p36.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 1(1P36.21) MUTATED	22	5	0	0
AMP PEAK 1(1P36.21) WILD-TYPE	162	232	64	165

Figure S2. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1p36.21' versus 'RPPA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.041

Table S3. Gene #1: 'amp_1p36.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 1(1P36.21) MUTATED	12	6	20
AMP PEAK 1(1P36.21) WILD-TYPE	212	198	198

Figure S3. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.039

Table S4. Gene #1: 'amp_1p36.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 1(1P36.21) MUTATED	14	21	3
AMP PEAK 1(1P36.21) WILD-TYPE	220	233	155

Figure S4. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S5. Gene #1: 'amp_1p36.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 1(1P36.21) MUTATED	37	3	0
AMP PEAK 1(1P36.21) WILD-TYPE	196	232	192

Figure S5. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S6. Gene #1: 'amp_1p36.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 1(1P36.21) MUTATED	35	5	0
AMP PEAK 1(1P36.21) WILD-TYPE	168	185	267

Figure S6. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1p36.21' versus 'MIRSEQ_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.025

Table S7. Gene #1: 'amp_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 1(1P36.21) MUTATED	7	4	1	0
AMP PEAK 1(1P36.21) WILD-TYPE	130	103	182	82

Figure S7. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S8. Gene #1: 'amp_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 1(1P36.21) MUTATED	3	0	9
AMP PEAK 1(1P36.21) WILD-TYPE	219	184	94

Figure S8. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.059

Table S9. Gene #1: 'amp_1p36.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 1(1P36.21) MUTATED	9	1	2
AMP PEAK 1(1P36.21) WILD-TYPE	176	160	157

Figure S9. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.002

Table S10. Gene #1: 'amp_1p36.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 1(1P36.21) MUTATED	1	2	1	8
AMP PEAK 1(1P36.21) WILD-TYPE	90	135	187	81

Figure S10. Get High-res Image Gene #1: 'amp_1p36.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'MRNA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.025

Table S11. Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 2(1Q22) MUTATED	26	28	19	19
AMP PEAK 2(1Q22) WILD-TYPE	121	68	133	94

Figure S11. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q22' versus 'MRNA_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.046

Table S12. Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 2(1Q22) MUTATED	27	25	9	31
AMP PEAK 2(1Q22) WILD-TYPE	121	77	91	127

Figure S12. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q22' versus 'MIR_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.071

Table S13. Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 2(1Q22) MUTATED	18	40	13	26
AMP PEAK 2(1Q22) WILD-TYPE	138	143	74	94

Figure S13. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S14. Gene #2: 'amp_1q22' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 2(1Q22) MUTATED	92	45	7
AMP PEAK 2(1Q22) WILD-TYPE	441	497	8

Figure S14. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00056

Table S15. Gene #2: 'amp_1q22' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 2(1Q22) MUTATED	31	19	1	8
AMP PEAK 2(1Q22) WILD-TYPE	153	218	63	157

Figure S15. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q22' versus 'RPPA_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.063

Table S16. Gene #2: 'amp_1q22' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 2(1Q22) MUTATED	18	18	33
AMP PEAK 2(1Q22) WILD-TYPE	206	186	185

Figure S16. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S17. Gene #2: 'amp_1q22' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 2(1Q22) MUTATED	44	15	11
AMP PEAK 2(1Q22) WILD-TYPE	189	220	181

Figure S17. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00023

Table S18. Gene #2: 'amp_1q22' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 2(1Q22) MUTATED	37	19	14
AMP PEAK 2(1Q22) WILD-TYPE	166	171	253

Figure S18. Get High-res Image Gene #2: 'amp_1q22' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S19. Gene #3: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 3(1Q32.1) MUTATED	163	35	7
AMP PEAK 3(1Q32.1) WILD-TYPE	370	507	8

Figure S19. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q32.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S20. Gene #3: 'amp_1q32.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 3(1Q32.1) MUTATED	53	12	6	6
AMP PEAK 3(1Q32.1) WILD-TYPE	131	225	58	159

Figure S20. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S21. Gene #3: 'amp_1q32.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 3(1Q32.1) MUTATED	62	6	16
AMP PEAK 3(1Q32.1) WILD-TYPE	171	229	176

Figure S21. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1q32.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S22. Gene #3: 'amp_1q32.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 3(1Q32.1) MUTATED	58	8	18
AMP PEAK 3(1Q32.1) WILD-TYPE	145	182	249

Figure S22. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S23. Gene #3: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 3(1Q32.1) MUTATED	8	14	23
AMP PEAK 3(1Q32.1) WILD-TYPE	214	170	80

Figure S23. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.002

Table S24. Gene #3: 'amp_1q32.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 3(1Q32.1) MUTATED	24	4	17
AMP PEAK 3(1Q32.1) WILD-TYPE	161	157	142

Figure S24. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_1q32.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S25. Gene #3: 'amp_1q32.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 3(1Q32.1) MUTATED	5	3	14	23
AMP PEAK 3(1Q32.1) WILD-TYPE	86	134	174	66

Figure S25. Get High-res Image Gene #3: 'amp_1q32.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S26. Gene #4: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 4(1Q44) MUTATED	96	28	5
AMP PEAK 4(1Q44) WILD-TYPE	437	514	10

Figure S26. Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #5: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00023

Table S27. Gene #4: 'amp_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 4(1Q44) MUTATED	27	12	1	5
AMP PEAK 4(1Q44) WILD-TYPE	157	225	63	160

Figure S27. Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_1q44' versus 'RPPA_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.047

Table S28. Gene #4: 'amp_1q44' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 4(1Q44) MUTATED	12	15	27
AMP PEAK 4(1Q44) WILD-TYPE	212	189	191

Figure S28. Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S29. Gene #4: 'amp_1q44' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 4(1Q44) MUTATED	39	7	10
AMP PEAK 4(1Q44) WILD-TYPE	194	228	182

Figure S29. Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S30. Gene #4: 'amp_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 4(1Q44) MUTATED	35	9	12
AMP PEAK 4(1Q44) WILD-TYPE	168	181	255

Figure S30. Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.04

Table S31. Gene #4: 'amp_1q44' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 4(1Q44) MUTATED	8	10	12
AMP PEAK 4(1Q44) WILD-TYPE	214	174	91

Figure S31. Get High-res Image Gene #4: 'amp_1q44' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.033

Table S32. Gene #5: 'amp_2p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 5(2P24.3) MUTATED	11	17	4	13
AMP PEAK 5(2P24.3) WILD-TYPE	137	85	96	145

Figure S32. Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.053

Table S33. Gene #5: 'amp_2p24.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 5(2P24.3) MUTATED	44	26	2
AMP PEAK 5(2P24.3) WILD-TYPE	489	516	13

Figure S33. Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.012

Table S34. Gene #5: 'amp_2p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 5(2P24.3) MUTATED	23	8	7
AMP PEAK 5(2P24.3) WILD-TYPE	210	227	185

Figure S34. Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00774 (Fisher's exact test), Q value = 0.016

Table S35. Gene #5: 'amp_2p24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 5(2P24.3) MUTATED	20	10	8
AMP PEAK 5(2P24.3) WILD-TYPE	183	180	259

Figure S35. Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.051

Table S36. Gene #5: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 5(2P24.3) MUTATED	8	5	10
AMP PEAK 5(2P24.3) WILD-TYPE	214	179	93

Figure S36. Get High-res Image Gene #5: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.3' versus 'MRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0013

Table S37. Gene #6: 'amp_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 6(3P25.3) MUTATED	15	21	7	13
AMP PEAK 6(3P25.3) WILD-TYPE	132	75	145	100

Figure S37. Get High-res Image Gene #6: 'amp_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3p25.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.028

Table S38. Gene #6: 'amp_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 6(3P25.3) MUTATED	10	19	7	20
AMP PEAK 6(3P25.3) WILD-TYPE	138	83	93	138

Figure S38. Get High-res Image Gene #6: 'amp_3p25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3p25.3' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.022

Table S39. Gene #6: 'amp_3p25.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 6(3P25.3) MUTATED	12	20	1	3
AMP PEAK 6(3P25.3) WILD-TYPE	172	217	63	162

Figure S39. Get High-res Image Gene #6: 'amp_3p25.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_3p25.3' versus 'RPPA_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.071

Table S40. Gene #6: 'amp_3p25.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 6(3P25.3) MUTATED	13	5	17
AMP PEAK 6(3P25.3) WILD-TYPE	211	199	201

Figure S40. Get High-res Image Gene #6: 'amp_3p25.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.041

Table S41. Gene #6: 'amp_3p25.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 6(3P25.3) MUTATED	20	15	10
AMP PEAK 6(3P25.3) WILD-TYPE	183	175	257

Figure S41. Get High-res Image Gene #6: 'amp_3p25.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.016

Table S42. Gene #7: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 7(3Q26.33) MUTATED	27	28	19	27
AMP PEAK 7(3Q26.33) WILD-TYPE	120	68	133	86

Figure S42. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S43. Gene #7: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 7(3Q26.33) MUTATED	108	22	2
AMP PEAK 7(3Q26.33) WILD-TYPE	425	520	13

Figure S43. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S44. Gene #7: 'amp_3q26.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 7(3Q26.33) MUTATED	31	9	2	3
AMP PEAK 7(3Q26.33) WILD-TYPE	153	228	62	162

Figure S44. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.00985 (Fisher's exact test), Q value = 0.02

Table S45. Gene #7: 'amp_3q26.33' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 7(3Q26.33) MUTATED	18	8	26
AMP PEAK 7(3Q26.33) WILD-TYPE	206	196	192

Figure S45. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_3q26.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00691 (Fisher's exact test), Q value = 0.014

Table S46. Gene #7: 'amp_3q26.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 7(3Q26.33) MUTATED	24	24	4
AMP PEAK 7(3Q26.33) WILD-TYPE	210	230	154

Figure S46. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S47. Gene #7: 'amp_3q26.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 7(3Q26.33) MUTATED	45	7	4
AMP PEAK 7(3Q26.33) WILD-TYPE	188	228	188

Figure S47. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S48. Gene #7: 'amp_3q26.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 7(3Q26.33) MUTATED	41	9	6
AMP PEAK 7(3Q26.33) WILD-TYPE	162	181	261

Figure S48. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.0079

Table S49. Gene #7: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 7(3Q26.33) MUTATED	10	7	1	3
AMP PEAK 7(3Q26.33) WILD-TYPE	127	100	182	79

Figure S49. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.035

Table S50. Gene #7: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 7(3Q26.33) MUTATED	9	3	9
AMP PEAK 7(3Q26.33) WILD-TYPE	213	181	94

Figure S50. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.04

Table S51. Gene #7: 'amp_3q26.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 7(3Q26.33) MUTATED	14	4	3
AMP PEAK 7(3Q26.33) WILD-TYPE	171	157	156

Figure S51. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0048

Table S52. Gene #7: 'amp_3q26.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 7(3Q26.33) MUTATED	6	1	5	9
AMP PEAK 7(3Q26.33) WILD-TYPE	85	136	183	80

Figure S52. Get High-res Image Gene #7: 'amp_3q26.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0018

Table S53. Gene #8: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 8(4P16.3) MUTATED	48	20	2
AMP PEAK 8(4P16.3) WILD-TYPE	485	522	13

Figure S53. Get High-res Image Gene #8: 'amp_4p16.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 0.0038 (Fisher's exact test), Q value = 0.0085

Table S54. Gene #8: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 8(4P16.3) MUTATED	15	13	2	1
AMP PEAK 8(4P16.3) WILD-TYPE	169	224	62	164

Figure S54. Get High-res Image Gene #8: 'amp_4p16.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S55. Gene #8: 'amp_4p16.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 8(4P16.3) MUTATED	25	10	3
AMP PEAK 8(4P16.3) WILD-TYPE	208	225	189

Figure S55. Get High-res Image Gene #8: 'amp_4p16.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00059

Table S56. Gene #8: 'amp_4p16.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 8(4P16.3) MUTATED	22	11	5
AMP PEAK 8(4P16.3) WILD-TYPE	181	179	262

Figure S56. Get High-res Image Gene #8: 'amp_4p16.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MRNA_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0018

Table S57. Gene #9: 'amp_4q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 9(4Q12) MUTATED	22	32	20	25
AMP PEAK 9(4Q12) WILD-TYPE	125	64	132	88

Figure S57. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00323 (Fisher's exact test), Q value = 0.0074

Table S58. Gene #9: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 9(4Q12) MUTATED	18	31	16	34
AMP PEAK 9(4Q12) WILD-TYPE	130	71	84	124

Figure S58. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S59. Gene #9: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 9(4Q12) MUTATED	100	35	3
AMP PEAK 9(4Q12) WILD-TYPE	433	507	12

Figure S59. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_4q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S60. Gene #9: 'amp_4q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 9(4Q12) MUTATED	31	21	2	1
AMP PEAK 9(4Q12) WILD-TYPE	153	216	62	164

Figure S60. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_4q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S61. Gene #9: 'amp_4q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 9(4Q12) MUTATED	44	10	5
AMP PEAK 9(4Q12) WILD-TYPE	189	225	187

Figure S61. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_4q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S62. Gene #9: 'amp_4q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 9(4Q12) MUTATED	37	16	6
AMP PEAK 9(4Q12) WILD-TYPE	166	174	261

Figure S62. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.007

Table S63. Gene #9: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 9(4Q12) MUTATED	6	15	7	2
AMP PEAK 9(4Q12) WILD-TYPE	131	92	176	80

Figure S63. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_4q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00048

Table S64. Gene #9: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 9(4Q12) MUTATED	7	7	16
AMP PEAK 9(4Q12) WILD-TYPE	215	177	87

Figure S64. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00393 (Fisher's exact test), Q value = 0.0087

Table S65. Gene #9: 'amp_4q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 9(4Q12) MUTATED	3	8	6	13
AMP PEAK 9(4Q12) WILD-TYPE	88	129	182	76

Figure S65. Get High-res Image Gene #9: 'amp_4q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.06

Table S66. Gene #10: 'amp_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 10(5P15.33) MUTATED	24	9	9	11
AMP PEAK 10(5P15.33) WILD-TYPE	123	87	143	102

Figure S66. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S67. Gene #10: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 10(5P15.33) MUTATED	55	19	2
AMP PEAK 10(5P15.33) WILD-TYPE	478	523	13

Figure S67. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 0.0093 (Fisher's exact test), Q value = 0.019

Table S68. Gene #10: 'amp_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 10(5P15.33) MUTATED	12	7	4	1
AMP PEAK 10(5P15.33) WILD-TYPE	172	230	60	164

Figure S68. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S69. Gene #10: 'amp_5p15.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 10(5P15.33) MUTATED	21	3	3
AMP PEAK 10(5P15.33) WILD-TYPE	212	232	189

Figure S69. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00094

Table S70. Gene #10: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 10(5P15.33) MUTATED	18	5	4
AMP PEAK 10(5P15.33) WILD-TYPE	185	185	263

Figure S70. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0032 (Fisher's exact test), Q value = 0.0073

Table S71. Gene #10: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 10(5P15.33) MUTATED	3	4	9
AMP PEAK 10(5P15.33) WILD-TYPE	219	180	94

Figure S71. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0374 (Fisher's exact test), Q value = 0.065

Table S72. Gene #10: 'amp_5p15.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 10(5P15.33) MUTATED	1	5	3	7
AMP PEAK 10(5P15.33) WILD-TYPE	90	132	185	82

Figure S72. Get High-res Image Gene #10: 'amp_5p15.33' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S73. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 11(7P11.2) MUTATED	139	68	147	89
AMP PEAK 11(7P11.2) WILD-TYPE	8	28	5	24

Figure S73. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S74. Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 11(7P11.2) MUTATED	136	60	99	148
AMP PEAK 11(7P11.2) WILD-TYPE	12	42	1	10

Figure S74. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'MIR_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S75. Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 11(7P11.2) MUTATED	151	146	73	110
AMP PEAK 11(7P11.2) WILD-TYPE	5	37	14	10

Figure S75. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7p11.2' versus 'MIR_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S76. Gene #11: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 11(7P11.2) MUTATED	234	120	126
AMP PEAK 11(7P11.2) WILD-TYPE	59	4	3

Figure S76. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S77. Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 11(7P11.2) MUTATED	519	106	10
AMP PEAK 11(7P11.2) WILD-TYPE	14	436	5

Figure S77. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S78. Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 11(7P11.2) MUTATED	167	43	26	14
AMP PEAK 11(7P11.2) WILD-TYPE	17	194	38	151

Figure S78. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S79. Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 11(7P11.2) MUTATED	104	70	124
AMP PEAK 11(7P11.2) WILD-TYPE	120	134	94

Figure S79. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S80. Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 11(7P11.2) MUTATED	120	128	50
AMP PEAK 11(7P11.2) WILD-TYPE	114	126	108

Figure S80. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S81. Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 11(7P11.2) MUTATED	185	37	37
AMP PEAK 11(7P11.2) WILD-TYPE	48	198	155

Figure S81. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S82. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 11(7P11.2) MUTATED	183	30	46
AMP PEAK 11(7P11.2) WILD-TYPE	20	160	221

Figure S82. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00092

Table S83. Gene #11: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 11(7P11.2) MUTATED	44	37	32	13
AMP PEAK 11(7P11.2) WILD-TYPE	93	70	151	69

Figure S83. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S84. Gene #11: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 11(7P11.2) MUTATED	37	28	61
AMP PEAK 11(7P11.2) WILD-TYPE	185	156	42

Figure S84. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S85. Gene #11: 'amp_7p11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 11(7P11.2) MUTATED	66	26	33
AMP PEAK 11(7P11.2) WILD-TYPE	119	135	126

Figure S85. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S86. Gene #11: 'amp_7p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 11(7P11.2) MUTATED	13	22	32	58
AMP PEAK 11(7P11.2) WILD-TYPE	78	115	156	31

Figure S86. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S87. Gene #12: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 12(7Q11.21) MUTATED	133	64	124	82
AMP PEAK 12(7Q11.21) WILD-TYPE	14	32	28	31

Figure S87. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S88. Gene #12: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 12(7Q11.21) MUTATED	129	55	82	137
AMP PEAK 12(7Q11.21) WILD-TYPE	19	47	18	21

Figure S88. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q11.21' versus 'MIR_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S89. Gene #12: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 12(7Q11.21) MUTATED	141	133	63	103
AMP PEAK 12(7Q11.21) WILD-TYPE	15	50	24	17

Figure S89. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q11.21' versus 'MIR_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S90. Gene #12: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 12(7Q11.21) MUTATED	216	114	110
AMP PEAK 12(7Q11.21) WILD-TYPE	77	10	19

Figure S90. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S91. Gene #12: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 12(7Q11.21) MUTATED	475	96	10
AMP PEAK 12(7Q11.21) WILD-TYPE	58	446	5

Figure S91. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S92. Gene #12: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 12(7Q11.21) MUTATED	155	39	23	14
AMP PEAK 12(7Q11.21) WILD-TYPE	29	198	41	151

Figure S92. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q11.21' versus 'RPPA_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0029

Table S93. Gene #12: 'amp_7q11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 12(7Q11.21) MUTATED	96	67	110
AMP PEAK 12(7Q11.21) WILD-TYPE	128	137	108

Figure S93. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0025

Table S94. Gene #12: 'amp_7q11.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 12(7Q11.21) MUTATED	111	115	47
AMP PEAK 12(7Q11.21) WILD-TYPE	123	139	111

Figure S94. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S95. Gene #12: 'amp_7q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 12(7Q11.21) MUTATED	164	34	37
AMP PEAK 12(7Q11.21) WILD-TYPE	69	201	155

Figure S95. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S96. Gene #12: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 12(7Q11.21) MUTATED	163	26	46
AMP PEAK 12(7Q11.21) WILD-TYPE	40	164	221

Figure S96. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.0098

Table S97. Gene #12: 'amp_7q11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 12(7Q11.21) MUTATED	40	32	31	12
AMP PEAK 12(7Q11.21) WILD-TYPE	97	75	152	70

Figure S97. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S98. Gene #12: 'amp_7q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 12(7Q11.21) MUTATED	34	27	54
AMP PEAK 12(7Q11.21) WILD-TYPE	188	157	49

Figure S98. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00067

Table S99. Gene #12: 'amp_7q11.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 12(7Q11.21) MUTATED	59	22	33
AMP PEAK 12(7Q11.21) WILD-TYPE	126	139	126

Figure S99. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S100. Gene #12: 'amp_7q11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 12(7Q11.21) MUTATED	11	20	32	51
AMP PEAK 12(7Q11.21) WILD-TYPE	80	117	156	38

Figure S100. Get High-res Image Gene #12: 'amp_7q11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S101. Gene #13: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 13(7Q21.2) MUTATED	131	64	134	89
AMP PEAK 13(7Q21.2) WILD-TYPE	16	32	18	24

Figure S101. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S102. Gene #13: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 13(7Q21.2) MUTATED	126	62	89	141
AMP PEAK 13(7Q21.2) WILD-TYPE	22	40	11	17

Figure S102. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'MIR_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S103. Gene #13: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 13(7Q21.2) MUTATED	224	111	117
AMP PEAK 13(7Q21.2) WILD-TYPE	69	13	12

Figure S103. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S104. Gene #13: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 13(7Q21.2) MUTATED	486	139	11
AMP PEAK 13(7Q21.2) WILD-TYPE	47	403	4

Figure S104. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S105. Gene #13: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 13(7Q21.2) MUTATED	158	69	25	24
AMP PEAK 13(7Q21.2) WILD-TYPE	26	168	39	141

Figure S105. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'RPPA_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.011

Table S106. Gene #13: 'amp_7q21.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 13(7Q21.2) MUTATED	107	81	121
AMP PEAK 13(7Q21.2) WILD-TYPE	117	123	97

Figure S106. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.024

Table S107. Gene #13: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 13(7Q21.2) MUTATED	124	125	60
AMP PEAK 13(7Q21.2) WILD-TYPE	110	129	98

Figure S107. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S108. Gene #13: 'amp_7q21.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 13(7Q21.2) MUTATED	175	57	50
AMP PEAK 13(7Q21.2) WILD-TYPE	58	178	142

Figure S108. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S109. Gene #13: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 13(7Q21.2) MUTATED	171	48	63
AMP PEAK 13(7Q21.2) WILD-TYPE	32	142	204

Figure S109. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.009

Table S110. Gene #13: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 13(7Q21.2) MUTATED	51	41	46	16
AMP PEAK 13(7Q21.2) WILD-TYPE	86	66	137	66

Figure S110. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S111. Gene #13: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 13(7Q21.2) MUTATED	52	43	59
AMP PEAK 13(7Q21.2) WILD-TYPE	170	141	44

Figure S111. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0022

Table S112. Gene #13: 'amp_7q21.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 13(7Q21.2) MUTATED	72	33	48
AMP PEAK 13(7Q21.2) WILD-TYPE	113	128	111

Figure S112. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S113. Gene #13: 'amp_7q21.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 13(7Q21.2) MUTATED	20	28	50	55
AMP PEAK 13(7Q21.2) WILD-TYPE	71	109	138	34

Figure S113. Get High-res Image Gene #13: 'amp_7q21.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0029

Table S114. Gene #14: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 14(7Q31.2) MUTATED	131	66	126	89
AMP PEAK 14(7Q31.2) WILD-TYPE	16	30	26	24

Figure S114. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S115. Gene #14: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 14(7Q31.2) MUTATED	130	63	83	136
AMP PEAK 14(7Q31.2) WILD-TYPE	18	39	17	22

Figure S115. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q31.2' versus 'MIR_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.026

Table S116. Gene #14: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 14(7Q31.2) MUTATED	137	136	71	101
AMP PEAK 14(7Q31.2) WILD-TYPE	19	47	16	19

Figure S116. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_7q31.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00906 (Fisher's exact test), Q value = 0.018

Table S117. Gene #14: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 14(7Q31.2) MUTATED	225	109	111
AMP PEAK 14(7Q31.2) WILD-TYPE	68	15	18

Figure S117. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S118. Gene #14: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 14(7Q31.2) MUTATED	478	157	11
AMP PEAK 14(7Q31.2) WILD-TYPE	55	385	4

Figure S118. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S119. Gene #14: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 14(7Q31.2) MUTATED	157	82	26	28
AMP PEAK 14(7Q31.2) WILD-TYPE	27	155	38	137

Figure S119. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.017

Table S120. Gene #14: 'amp_7q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 14(7Q31.2) MUTATED	114	84	122
AMP PEAK 14(7Q31.2) WILD-TYPE	110	120	96

Figure S120. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.025 (Fisher's exact test), Q value = 0.045

Table S121. Gene #14: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 14(7Q31.2) MUTATED	127	129	64
AMP PEAK 14(7Q31.2) WILD-TYPE	107	125	94

Figure S121. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S122. Gene #14: 'amp_7q31.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 14(7Q31.2) MUTATED	172	68	56
AMP PEAK 14(7Q31.2) WILD-TYPE	61	167	136

Figure S122. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S123. Gene #14: 'amp_7q31.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 14(7Q31.2) MUTATED	168	57	71
AMP PEAK 14(7Q31.2) WILD-TYPE	35	133	196

Figure S123. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.02

Table S124. Gene #14: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 14(7Q31.2) MUTATED	56	44	52	20
AMP PEAK 14(7Q31.2) WILD-TYPE	81	63	131	62

Figure S124. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S125. Gene #14: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 14(7Q31.2) MUTATED	65	48	59
AMP PEAK 14(7Q31.2) WILD-TYPE	157	136	44

Figure S125. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.017

Table S126. Gene #14: 'amp_7q31.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 14(7Q31.2) MUTATED	76	41	54
AMP PEAK 14(7Q31.2) WILD-TYPE	109	120	105

Figure S126. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S127. Gene #14: 'amp_7q31.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 14(7Q31.2) MUTATED	24	35	57	55
AMP PEAK 14(7Q31.2) WILD-TYPE	67	102	131	34

Figure S127. Get High-res Image Gene #14: 'amp_7q31.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q32.3' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00064

Table S128. Gene #15: 'amp_7q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 15(7Q32.3) MUTATED	131	64	129	92
AMP PEAK 15(7Q32.3) WILD-TYPE	16	32	23	21

Figure S128. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_7q32.3' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S129. Gene #15: 'amp_7q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 15(7Q32.3) MUTATED	127	66	86	137
AMP PEAK 15(7Q32.3) WILD-TYPE	21	36	14	21

Figure S129. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q32.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.01

Table S130. Gene #15: 'amp_7q32.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 15(7Q32.3) MUTATED	227	110	113
AMP PEAK 15(7Q32.3) WILD-TYPE	66	14	16

Figure S130. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_7q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S131. Gene #15: 'amp_7q32.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 15(7Q32.3) MUTATED	479	169	11
AMP PEAK 15(7Q32.3) WILD-TYPE	54	373	4

Figure S131. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_7q32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S132. Gene #15: 'amp_7q32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 15(7Q32.3) MUTATED	157	87	27	29
AMP PEAK 15(7Q32.3) WILD-TYPE	27	150	37	136

Figure S132. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_7q32.3' versus 'RPPA_CNMF'

P value = 0.00531 (Fisher's exact test), Q value = 0.011

Table S133. Gene #15: 'amp_7q32.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 15(7Q32.3) MUTATED	118	87	127
AMP PEAK 15(7Q32.3) WILD-TYPE	106	117	91

Figure S133. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_7q32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.03

Table S134. Gene #15: 'amp_7q32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 15(7Q32.3) MUTATED	132	134	66
AMP PEAK 15(7Q32.3) WILD-TYPE	102	120	92

Figure S134. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_7q32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S135. Gene #15: 'amp_7q32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 15(7Q32.3) MUTATED	172	72	60
AMP PEAK 15(7Q32.3) WILD-TYPE	61	163	132

Figure S135. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_7q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S136. Gene #15: 'amp_7q32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 15(7Q32.3) MUTATED	168	60	76
AMP PEAK 15(7Q32.3) WILD-TYPE	35	130	191

Figure S136. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S137. Gene #15: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 15(7Q32.3) MUTATED	68	52	60
AMP PEAK 15(7Q32.3) WILD-TYPE	154	132	43

Figure S137. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.04

Table S138. Gene #15: 'amp_7q32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 15(7Q32.3) MUTATED	78	45	56
AMP PEAK 15(7Q32.3) WILD-TYPE	107	116	103

Figure S138. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_7q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S139. Gene #15: 'amp_7q32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 15(7Q32.3) MUTATED	28	37	59	55
AMP PEAK 15(7Q32.3) WILD-TYPE	63	100	129	34

Figure S139. Get High-res Image Gene #15: 'amp_7q32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S140. Gene #16: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 16(8Q24.21) MUTATED	8	25	7	21
AMP PEAK 16(8Q24.21) WILD-TYPE	139	71	145	92

Figure S140. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S141. Gene #16: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 16(8Q24.21) MUTATED	10	29	6	16
AMP PEAK 16(8Q24.21) WILD-TYPE	138	73	94	142

Figure S141. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'MIR_CNMF'

P value = 0.0161 (Fisher's exact test), Q value = 0.03

Table S142. Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 16(8Q24.21) MUTATED	11	32	11	10
AMP PEAK 16(8Q24.21) WILD-TYPE	145	151	76	110

Figure S142. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S143. Gene #16: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 16(8Q24.21) MUTATED	50	114	5
AMP PEAK 16(8Q24.21) WILD-TYPE	483	428	10

Figure S143. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S144. Gene #16: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 16(8Q24.21) MUTATED	13	86	5	10
AMP PEAK 16(8Q24.21) WILD-TYPE	171	151	59	155

Figure S144. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0017

Table S145. Gene #16: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 16(8Q24.21) MUTATED	29	61	31
AMP PEAK 16(8Q24.21) WILD-TYPE	204	174	161

Figure S145. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S146. Gene #16: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 16(8Q24.21) MUTATED	21	63	37
AMP PEAK 16(8Q24.21) WILD-TYPE	182	127	230

Figure S146. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0023

Table S147. Gene #16: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 16(8Q24.21) MUTATED	58	30	10
AMP PEAK 16(8Q24.21) WILD-TYPE	164	154	93

Figure S147. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S148. Gene #16: 'amp_8q24.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 16(8Q24.21) MUTATED	33	21	36	8
AMP PEAK 16(8Q24.21) WILD-TYPE	58	116	152	81

Figure S148. Get High-res Image Gene #16: 'amp_8q24.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNA_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.013

Table S149. Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 17(9Q34.3) MUTATED	24	28	18	17
AMP PEAK 17(9Q34.3) WILD-TYPE	123	68	134	96

Figure S149. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_9q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00608 (Fisher's exact test), Q value = 0.013

Table S150. Gene #17: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 17(9Q34.3) MUTATED	23	28	9	27
AMP PEAK 17(9Q34.3) WILD-TYPE	125	74	91	131

Figure S150. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0045

Table S151. Gene #17: 'amp_9q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 17(9Q34.3) MUTATED	84	52	4
AMP PEAK 17(9Q34.3) WILD-TYPE	449	490	11

Figure S151. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.068

Table S152. Gene #17: 'amp_9q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 17(9Q34.3) MUTATED	21	30	3	9
AMP PEAK 17(9Q34.3) WILD-TYPE	163	207	61	156

Figure S152. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.053

Table S153. Gene #17: 'amp_9q34.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 17(9Q34.3) MUTATED	15	19	31
AMP PEAK 17(9Q34.3) WILD-TYPE	209	185	187

Figure S153. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.021

Table S154. Gene #17: 'amp_9q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 17(9Q34.3) MUTATED	37	21	14
AMP PEAK 17(9Q34.3) WILD-TYPE	196	214	178

Figure S154. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.033

Table S155. Gene #17: 'amp_9q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 17(9Q34.3) MUTATED	31	22	19
AMP PEAK 17(9Q34.3) WILD-TYPE	172	168	248

Figure S155. Get High-res Image Gene #17: 'amp_9q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00046

Table S156. Gene #18: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 18(10P15.1) MUTATED	1	8	1	8
AMP PEAK 18(10P15.1) WILD-TYPE	146	88	151	105

Figure S156. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S157. Gene #18: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 18(10P15.1) MUTATED	2	13	1	2
AMP PEAK 18(10P15.1) WILD-TYPE	146	89	99	156

Figure S157. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'MIR_CNMF'

P value = 0.00545 (Fisher's exact test), Q value = 0.012

Table S158. Gene #18: 'amp_10p15.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 18(10P15.1) MUTATED	1	12	3	1
AMP PEAK 18(10P15.1) WILD-TYPE	155	171	84	119

Figure S158. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S159. Gene #18: 'amp_10p15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 18(10P15.1) MUTATED	6	82	0
AMP PEAK 18(10P15.1) WILD-TYPE	527	460	15

Figure S159. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S160. Gene #18: 'amp_10p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 18(10P15.1) MUTATED	2	65	4	0
AMP PEAK 18(10P15.1) WILD-TYPE	182	172	60	165

Figure S160. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S161. Gene #18: 'amp_10p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 18(10P15.1) MUTATED	9	45	18
AMP PEAK 18(10P15.1) WILD-TYPE	224	190	174

Figure S161. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S162. Gene #18: 'amp_10p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 18(10P15.1) MUTATED	3	50	19
AMP PEAK 18(10P15.1) WILD-TYPE	200	140	248

Figure S162. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S163. Gene #18: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 18(10P15.1) MUTATED	18	26	21	3
AMP PEAK 18(10P15.1) WILD-TYPE	119	81	162	79

Figure S163. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0023

Table S164. Gene #18: 'amp_10p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 18(10P15.1) MUTATED	25	15	21	7
AMP PEAK 18(10P15.1) WILD-TYPE	66	122	167	82

Figure S164. Get High-res Image Gene #18: 'amp_10p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00051

Table S165. Gene #19: 'amp_11p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 19(11P13) MUTATED	5	9	0	20
AMP PEAK 19(11P13) WILD-TYPE	179	228	64	145

Figure S165. Get High-res Image Gene #19: 'amp_11p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.041

Table S166. Gene #19: 'amp_11p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 19(11P13) MUTATED	5	9	15	0
AMP PEAK 19(11P13) WILD-TYPE	86	128	173	89

Figure S166. Get High-res Image Gene #19: 'amp_11p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q24.1' versus 'MRNA_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.0089

Table S167. Gene #20: 'amp_11q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 20(11Q24.1) MUTATED	4	7	2	11
AMP PEAK 20(11Q24.1) WILD-TYPE	143	89	150	102

Figure S167. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00771 (Fisher's exact test), Q value = 0.016

Table S168. Gene #20: 'amp_11q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 20(11Q24.1) MUTATED	4	11	1	8
AMP PEAK 20(11Q24.1) WILD-TYPE	144	91	99	150

Figure S168. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S169. Gene #20: 'amp_11q24.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 20(11Q24.1) MUTATED	20	90	2
AMP PEAK 20(11Q24.1) WILD-TYPE	513	452	13

Figure S169. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_11q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S170. Gene #20: 'amp_11q24.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 20(11Q24.1) MUTATED	10	52	2	29
AMP PEAK 20(11Q24.1) WILD-TYPE	174	185	62	136

Figure S170. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_11q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S171. Gene #20: 'amp_11q24.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 20(11Q24.1) MUTATED	14	50	29
AMP PEAK 20(11Q24.1) WILD-TYPE	219	185	163

Figure S171. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_11q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S172. Gene #20: 'amp_11q24.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 20(11Q24.1) MUTATED	8	39	46
AMP PEAK 20(11Q24.1) WILD-TYPE	195	151	221

Figure S172. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_11q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0437 (Fisher's exact test), Q value = 0.074

Table S173. Gene #20: 'amp_11q24.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 20(11Q24.1) MUTATED	20	24	36	7
AMP PEAK 20(11Q24.1) WILD-TYPE	71	113	152	82

Figure S173. Get High-res Image Gene #20: 'amp_11q24.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S174. Gene #21: 'amp_12p13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 21(12P13.32) MUTATED	23	59	1	4
AMP PEAK 21(12P13.32) WILD-TYPE	161	178	63	161

Figure S174. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12p13.32' versus 'RPPA_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0058

Table S175. Gene #21: 'amp_12p13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 21(12P13.32) MUTATED	20	22	43
AMP PEAK 21(12P13.32) WILD-TYPE	204	182	175

Figure S175. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_12p13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.023

Table S176. Gene #21: 'amp_12p13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 21(12P13.32) MUTATED	31	43	11
AMP PEAK 21(12P13.32) WILD-TYPE	203	211	147

Figure S176. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_12p13.32' versus 'MRNASEQ_CNMF'

P value = 0.00351 (Fisher's exact test), Q value = 0.0079

Table S177. Gene #21: 'amp_12p13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 21(12P13.32) MUTATED	35	42	14
AMP PEAK 21(12P13.32) WILD-TYPE	198	193	178

Figure S177. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12p13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S178. Gene #21: 'amp_12p13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 21(12P13.32) MUTATED	29	43	19
AMP PEAK 21(12P13.32) WILD-TYPE	174	147	248

Figure S178. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.32' versus 'MIRSEQ_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.0073

Table S179. Gene #21: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 21(12P13.32) MUTATED	17	26	16	9
AMP PEAK 21(12P13.32) WILD-TYPE	120	81	167	73

Figure S179. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_12p13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.0078

Table S180. Gene #21: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 21(12P13.32) MUTATED	35	13	20
AMP PEAK 21(12P13.32) WILD-TYPE	187	171	83

Figure S180. Get High-res Image Gene #21: 'amp_12p13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S181. Gene #22: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 22(12Q14.1) MUTATED	137	32	2
AMP PEAK 22(12Q14.1) WILD-TYPE	396	510	13

Figure S181. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S182. Gene #22: 'amp_12q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 22(12Q14.1) MUTATED	42	16	3	5
AMP PEAK 22(12Q14.1) WILD-TYPE	142	221	61	160

Figure S182. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S183. Gene #22: 'amp_12q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 22(12Q14.1) MUTATED	64	11	4
AMP PEAK 22(12Q14.1) WILD-TYPE	169	224	188

Figure S183. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S184. Gene #22: 'amp_12q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 22(12Q14.1) MUTATED	58	13	8
AMP PEAK 22(12Q14.1) WILD-TYPE	145	177	259

Figure S184. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_CNMF'

P value = 0.0028 (Fisher's exact test), Q value = 0.0065

Table S185. Gene #22: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 22(12Q14.1) MUTATED	13	15	6	3
AMP PEAK 22(12Q14.1) WILD-TYPE	124	92	177	79

Figure S185. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_12q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S186. Gene #22: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 22(12Q14.1) MUTATED	10	5	22
AMP PEAK 22(12Q14.1) WILD-TYPE	212	179	81

Figure S186. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.071

Table S187. Gene #22: 'amp_12q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 22(12Q14.1) MUTATED	21	8	8
AMP PEAK 22(12Q14.1) WILD-TYPE	164	153	151

Figure S187. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_12q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S188. Gene #22: 'amp_12q14.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 22(12Q14.1) MUTATED	6	5	7	19
AMP PEAK 22(12Q14.1) WILD-TYPE	85	132	181	70

Figure S188. Get High-res Image Gene #22: 'amp_12q14.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S189. Gene #23: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 23(12Q15) MUTATED	98	13	0
AMP PEAK 23(12Q15) WILD-TYPE	435	529	15

Figure S189. Get High-res Image Gene #23: 'amp_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S190. Gene #23: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 23(12Q15) MUTATED	28	4	2	4
AMP PEAK 23(12Q15) WILD-TYPE	156	233	62	161

Figure S190. Get High-res Image Gene #23: 'amp_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S191. Gene #23: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 23(12Q15) MUTATED	34	4	4
AMP PEAK 23(12Q15) WILD-TYPE	199	231	188

Figure S191. Get High-res Image Gene #23: 'amp_12q15' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S192. Gene #23: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 23(12Q15) MUTATED	34	1	7
AMP PEAK 23(12Q15) WILD-TYPE	169	189	260

Figure S192. Get High-res Image Gene #23: 'amp_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIR_CNMF'

P value = 0.0292 (Fisher's exact test), Q value = 0.052

Table S193. Gene #24: 'amp_13q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 24(13Q34) MUTATED	3	17	5	6
AMP PEAK 24(13Q34) WILD-TYPE	153	166	82	114

Figure S193. Get High-res Image Gene #24: 'amp_13q34' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.003

Table S194. Gene #24: 'amp_13q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 24(13Q34) MUTATED	6	19	1	1
AMP PEAK 24(13Q34) WILD-TYPE	178	218	63	164

Figure S194. Get High-res Image Gene #24: 'amp_13q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.048

Table S195. Gene #24: 'amp_13q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 24(13Q34) MUTATED	13	13	6
AMP PEAK 24(13Q34) WILD-TYPE	190	177	261

Figure S195. Get High-res Image Gene #24: 'amp_13q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00097

Table S196. Gene #25: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 25(14Q32.33) MUTATED	32	10	2
AMP PEAK 25(14Q32.33) WILD-TYPE	501	532	13

Figure S196. Get High-res Image Gene #25: 'amp_14q32.33' versus Molecular Subtype #5: 'CN_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.04

Table S197. Gene #25: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 25(14Q32.33) MUTATED	12	4	2
AMP PEAK 25(14Q32.33) WILD-TYPE	221	231	190

Figure S197. Get High-res Image Gene #25: 'amp_14q32.33' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.018

Table S198. Gene #25: 'amp_14q32.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 25(14Q32.33) MUTATED	11	5	2
AMP PEAK 25(14Q32.33) WILD-TYPE	192	185	265

Figure S198. Get High-res Image Gene #25: 'amp_14q32.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_17p13.2' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.002

Table S199. Gene #26: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 26(17P13.2) MUTATED	9	12	6	20
AMP PEAK 26(17P13.2) WILD-TYPE	138	84	146	93

Figure S199. Get High-res Image Gene #26: 'amp_17p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.027

Table S200. Gene #26: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 26(17P13.2) MUTATED	10	18	5	14
AMP PEAK 26(17P13.2) WILD-TYPE	138	84	95	144

Figure S200. Get High-res Image Gene #26: 'amp_17p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17p13.2' versus 'MIR_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.081

Table S201. Gene #26: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 26(17P13.2) MUTATED	6	21	8	13
AMP PEAK 26(17P13.2) WILD-TYPE	150	162	79	107

Figure S201. Get High-res Image Gene #26: 'amp_17p13.2' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_17p13.2' versus 'RPPA_CNMF'

P value = 0.00609 (Fisher's exact test), Q value = 0.013

Table S202. Gene #26: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 26(17P13.2) MUTATED	17	4	18
AMP PEAK 26(17P13.2) WILD-TYPE	207	200	200

Figure S202. Get High-res Image Gene #26: 'amp_17p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_17p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.058

Table S203. Gene #26: 'amp_17p13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 26(17P13.2) MUTATED	4	13	6
AMP PEAK 26(17P13.2) WILD-TYPE	181	148	153

Figure S203. Get High-res Image Gene #26: 'amp_17p13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.027

Table S204. Gene #27: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 27(17Q25.1) MUTATED	19	22	13	19
AMP PEAK 27(17Q25.1) WILD-TYPE	128	74	139	94

Figure S204. Get High-res Image Gene #27: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S205. Gene #27: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 27(17Q25.1) MUTATED	82	42	4
AMP PEAK 27(17Q25.1) WILD-TYPE	451	500	11

Figure S205. Get High-res Image Gene #27: 'amp_17q25.1' versus Molecular Subtype #5: 'CN_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.023

Table S206. Gene #27: 'amp_17q25.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 27(17Q25.1) MUTATED	32	22	10
AMP PEAK 27(17Q25.1) WILD-TYPE	201	213	182

Figure S206. Get High-res Image Gene #27: 'amp_17q25.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.06

Table S207. Gene #27: 'amp_17q25.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 27(17Q25.1) MUTATED	27	20	17
AMP PEAK 27(17Q25.1) WILD-TYPE	176	170	250

Figure S207. Get High-res Image Gene #27: 'amp_17q25.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S208. Gene #28: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 28(19P13.3) MUTATED	58	34	96	29
AMP PEAK 28(19P13.3) WILD-TYPE	89	62	56	84

Figure S208. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S209. Gene #28: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 28(19P13.3) MUTATED	67	31	62	57
AMP PEAK 28(19P13.3) WILD-TYPE	81	71	38	101

Figure S209. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.3' versus 'MIR_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.046

Table S210. Gene #28: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
AMP PEAK 28(19P13.3) MUTATED	67	88	25	52
AMP PEAK 28(19P13.3) WILD-TYPE	89	95	62	68

Figure S210. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #3: 'MIR_CNMF'

'amp_19p13.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0058

Table S211. Gene #28: 'amp_19p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 28(19P13.3) MUTATED	108	53	71
AMP PEAK 28(19P13.3) WILD-TYPE	185	71	58

Figure S211. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S212. Gene #28: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 28(19P13.3) MUTATED	252	117	6
AMP PEAK 28(19P13.3) WILD-TYPE	281	425	9

Figure S212. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S213. Gene #28: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 28(19P13.3) MUTATED	76	21	6	80
AMP PEAK 28(19P13.3) WILD-TYPE	108	216	58	85

Figure S213. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0265 (Fisher's exact test), Q value = 0.047

Table S214. Gene #28: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 28(19P13.3) MUTATED	69	91	37
AMP PEAK 28(19P13.3) WILD-TYPE	165	163	121

Figure S214. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0044

Table S215. Gene #28: 'amp_19p13.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 28(19P13.3) MUTATED	82	48	55
AMP PEAK 28(19P13.3) WILD-TYPE	151	187	137

Figure S215. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S216. Gene #28: 'amp_19p13.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 28(19P13.3) MUTATED	77	19	89
AMP PEAK 28(19P13.3) WILD-TYPE	126	171	178

Figure S216. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S217. Gene #28: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 28(19P13.3) MUTATED	24	23	45	37
AMP PEAK 28(19P13.3) WILD-TYPE	113	84	138	45

Figure S217. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.075

Table S218. Gene #28: 'amp_19p13.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 28(19P13.3) MUTATED	37	51	41
AMP PEAK 28(19P13.3) WILD-TYPE	148	110	118

Figure S218. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0021

Table S219. Gene #28: 'amp_19p13.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 28(19P13.3) MUTATED	10	46	47	26
AMP PEAK 28(19P13.3) WILD-TYPE	81	91	141	63

Figure S219. Get High-res Image Gene #28: 'amp_19p13.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S220. Gene #29: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 29(19P13.2) MUTATED	57	38	101	25
AMP PEAK 29(19P13.2) WILD-TYPE	90	58	51	88

Figure S220. Get High-res Image Gene #29: '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 = 3.8e-05

Table S221. Gene #29: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 29(19P13.2) MUTATED	66	32	66	57
AMP PEAK 29(19P13.2) WILD-TYPE	82	70	34	101

Figure S221. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'MIR_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0034

Table S222. Gene #29: 'amp_19p13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 29(19P13.2) MUTATED	109	54	73
AMP PEAK 29(19P13.2) WILD-TYPE	184	70	56

Figure S222. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S223. Gene #29: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 29(19P13.2) MUTATED	261	104	6
AMP PEAK 29(19P13.2) WILD-TYPE	272	438	9

Figure S223. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S224. Gene #29: 'amp_19p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 29(19P13.2) MUTATED	79	13	6	77
AMP PEAK 29(19P13.2) WILD-TYPE	105	224	58	88

Figure S224. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CNMF'

P value = 0.0177 (Fisher's exact test), Q value = 0.033

Table S225. Gene #29: 'amp_19p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 29(19P13.2) MUTATED	67	48	79
AMP PEAK 29(19P13.2) WILD-TYPE	157	156	139

Figure S225. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00655 (Fisher's exact test), Q value = 0.014

Table S226. Gene #29: 'amp_19p13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 29(19P13.2) MUTATED	71	90	33
AMP PEAK 29(19P13.2) WILD-TYPE	163	164	125

Figure S226. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S227. Gene #29: 'amp_19p13.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 29(19P13.2) MUTATED	88	43	48
AMP PEAK 29(19P13.2) WILD-TYPE	145	192	144

Figure S227. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S228. Gene #29: 'amp_19p13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 29(19P13.2) MUTATED	83	15	81
AMP PEAK 29(19P13.2) WILD-TYPE	120	175	186

Figure S228. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00069

Table S229. Gene #29: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 29(19P13.2) MUTATED	26	21	39	36
AMP PEAK 29(19P13.2) WILD-TYPE	111	86	144	46

Figure S229. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.07

Table S230. Gene #29: 'amp_19p13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 29(19P13.2) MUTATED	36	50	36
AMP PEAK 29(19P13.2) WILD-TYPE	149	111	123

Figure S230. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0015

Table S231. Gene #29: 'amp_19p13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 29(19P13.2) MUTATED	9	41	43	29
AMP PEAK 29(19P13.2) WILD-TYPE	82	96	145	60

Figure S231. Get High-res Image Gene #29: 'amp_19p13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S232. Gene #30: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 30(19Q12) MUTATED	55	31	85	17
AMP PEAK 30(19Q12) WILD-TYPE	92	65	67	96

Figure S232. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S233. Gene #30: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 30(19Q12) MUTATED	62	21	54	51
AMP PEAK 30(19Q12) WILD-TYPE	86	81	46	107

Figure S233. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'MIR_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.01

Table S234. Gene #30: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 30(19Q12) MUTATED	91	49	61
AMP PEAK 30(19Q12) WILD-TYPE	202	75	68

Figure S234. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S235. Gene #30: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 30(19Q12) MUTATED	221	20	6
AMP PEAK 30(19Q12) WILD-TYPE	312	522	9

Figure S235. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S236. Gene #30: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 30(19Q12) MUTATED	62	8	6	0
AMP PEAK 30(19Q12) WILD-TYPE	122	229	58	165

Figure S236. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.043

Table S237. Gene #30: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 30(19Q12) MUTATED	39	22	44
AMP PEAK 30(19Q12) WILD-TYPE	185	182	174

Figure S237. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0022

Table S238. Gene #30: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 30(19Q12) MUTATED	40	53	12
AMP PEAK 30(19Q12) WILD-TYPE	194	201	146

Figure S238. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S239. Gene #30: 'amp_19q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 30(19Q12) MUTATED	73	3	5
AMP PEAK 30(19Q12) WILD-TYPE	160	232	187

Figure S239. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S240. Gene #30: 'amp_19q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 30(19Q12) MUTATED	69	7	5
AMP PEAK 30(19Q12) WILD-TYPE	134	183	262

Figure S240. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00053

Table S241. Gene #30: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 30(19Q12) MUTATED	10	15	6	0
AMP PEAK 30(19Q12) WILD-TYPE	127	92	177	82

Figure S241. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S242. Gene #30: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 30(19Q12) MUTATED	6	2	23
AMP PEAK 30(19Q12) WILD-TYPE	216	182	80

Figure S242. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S243. Gene #30: 'amp_19q12' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 30(19Q12) MUTATED	23	3	5
AMP PEAK 30(19Q12) WILD-TYPE	162	158	154

Figure S243. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S244. Gene #30: 'amp_19q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 30(19Q12) MUTATED	3	3	2	23
AMP PEAK 30(19Q12) WILD-TYPE	88	134	186	66

Figure S244. Get High-res Image Gene #30: 'amp_19q12' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S245. Gene #31: 'amp_19q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
AMP PEAK 31(19Q13.2) MUTATED	52	27	78	14
AMP PEAK 31(19Q13.2) WILD-TYPE	95	69	74	99

Figure S245. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S246. Gene #31: 'amp_19q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
AMP PEAK 31(19Q13.2) MUTATED	62	18	49	42
AMP PEAK 31(19Q13.2) WILD-TYPE	86	84	51	116

Figure S246. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q13.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.014

Table S247. Gene #31: 'amp_19q13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
AMP PEAK 31(19Q13.2) MUTATED	83	47	56
AMP PEAK 31(19Q13.2) WILD-TYPE	210	77	73

Figure S247. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S248. Gene #31: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 31(19Q13.2) MUTATED	207	17	7
AMP PEAK 31(19Q13.2) WILD-TYPE	326	525	8

Figure S248. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #5: 'CN_CNMF'

'amp_19q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S249. Gene #31: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 31(19Q13.2) MUTATED	63	5	7	0
AMP PEAK 31(19Q13.2) WILD-TYPE	121	232	57	165

Figure S249. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_19q13.2' versus 'RPPA_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.01

Table S250. Gene #31: 'amp_19q13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
AMP PEAK 31(19Q13.2) MUTATED	34	16	40
AMP PEAK 31(19Q13.2) WILD-TYPE	190	188	178

Figure S250. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'amp_19q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.003

Table S251. Gene #31: 'amp_19q13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
AMP PEAK 31(19Q13.2) MUTATED	32	48	10
AMP PEAK 31(19Q13.2) WILD-TYPE	202	206	148

Figure S251. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'amp_19q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S252. Gene #31: 'amp_19q13.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 31(19Q13.2) MUTATED	67	3	5
AMP PEAK 31(19Q13.2) WILD-TYPE	166	232	187

Figure S252. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S253. Gene #31: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 31(19Q13.2) MUTATED	63	7	5
AMP PEAK 31(19Q13.2) WILD-TYPE	140	183	262

Figure S253. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.2' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00048

Table S254. Gene #31: 'amp_19q13.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 31(19Q13.2) MUTATED	13	13	5	0
AMP PEAK 31(19Q13.2) WILD-TYPE	124	94	178	82

Figure S254. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S255. Gene #31: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
AMP PEAK 31(19Q13.2) MUTATED	7	1	23
AMP PEAK 31(19Q13.2) WILD-TYPE	215	183	80

Figure S255. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S256. Gene #31: 'amp_19q13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
AMP PEAK 31(19Q13.2) MUTATED	25	2	4
AMP PEAK 31(19Q13.2) WILD-TYPE	160	159	155

Figure S256. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S257. Gene #31: 'amp_19q13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 31(19Q13.2) MUTATED	5	1	1	24
AMP PEAK 31(19Q13.2) WILD-TYPE	86	136	187	65

Figure S257. Get High-res Image Gene #31: 'amp_19q13.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.21' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S258. Gene #32: 'amp_xp11.21' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
AMP PEAK 32(XP11.21) MUTATED	29	74	1
AMP PEAK 32(XP11.21) WILD-TYPE	504	468	14

Figure S258. Get High-res Image Gene #32: 'amp_xp11.21' versus Molecular Subtype #5: 'CN_CNMF'

'amp_xp11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S259. Gene #32: 'amp_xp11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
AMP PEAK 32(XP11.21) MUTATED	7	63	5	1
AMP PEAK 32(XP11.21) WILD-TYPE	177	174	59	164

Figure S259. Get High-res Image Gene #32: 'amp_xp11.21' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'amp_xp11.21' versus 'MRNASEQ_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.007

Table S260. Gene #32: 'amp_xp11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
AMP PEAK 32(XP11.21) MUTATED	18	41	18
AMP PEAK 32(XP11.21) WILD-TYPE	215	194	174

Figure S260. Get High-res Image Gene #32: 'amp_xp11.21' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'amp_xp11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S261. Gene #32: 'amp_xp11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
AMP PEAK 32(XP11.21) MUTATED	9	49	19
AMP PEAK 32(XP11.21) WILD-TYPE	194	141	248

Figure S261. Get High-res Image Gene #32: 'amp_xp11.21' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.21' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00026

Table S262. Gene #32: 'amp_xp11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
AMP PEAK 32(XP11.21) MUTATED	26	21	21	1
AMP PEAK 32(XP11.21) WILD-TYPE	111	86	162	81

Figure S262. Get High-res Image Gene #32: 'amp_xp11.21' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'amp_xp11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0035 (Fisher's exact test), Q value = 0.0079

Table S263. Gene #32: 'amp_xp11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
AMP PEAK 32(XP11.21) MUTATED	24	14	22	9
AMP PEAK 32(XP11.21) WILD-TYPE	67	123	166	80

Figure S263. Get High-res Image Gene #32: 'amp_xp11.21' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S264. Gene #33: 'del_1p36.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 1(1P36.32) MUTATED	114	204	0
DEL PEAK 1(1P36.32) WILD-TYPE	419	338	15

Figure S264. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S265. Gene #33: 'del_1p36.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 1(1P36.32) MUTATED	39	11	17	164
DEL PEAK 1(1P36.32) WILD-TYPE	145	226	47	1

Figure S265. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.32' versus 'RPPA_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.02

Table S266. Gene #33: 'del_1p36.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 1(1P36.32) MUTATED	65	86	68
DEL PEAK 1(1P36.32) WILD-TYPE	159	118	150

Figure S266. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p36.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0014

Table S267. Gene #33: 'del_1p36.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 1(1P36.32) MUTATED	69	76	74
DEL PEAK 1(1P36.32) WILD-TYPE	165	178	84

Figure S267. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p36.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S268. Gene #33: 'del_1p36.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 1(1P36.32) MUTATED	38	84	106
DEL PEAK 1(1P36.32) WILD-TYPE	195	151	86

Figure S268. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p36.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S269. Gene #33: 'del_1p36.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 1(1P36.32) MUTATED	34	16	178
DEL PEAK 1(1P36.32) WILD-TYPE	169	174	89

Figure S269. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S270. Gene #33: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 1(1P36.32) MUTATED	33	13	92	68
DEL PEAK 1(1P36.32) WILD-TYPE	104	94	91	14

Figure S270. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p36.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S271. Gene #33: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 1(1P36.32) MUTATED	84	101	21
DEL PEAK 1(1P36.32) WILD-TYPE	138	83	82

Figure S271. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S272. Gene #33: 'del_1p36.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 1(1P36.32) MUTATED	44	83	79
DEL PEAK 1(1P36.32) WILD-TYPE	141	78	80

Figure S272. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S273. Gene #33: 'del_1p36.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 1(1P36.32) MUTATED	7	83	95	21
DEL PEAK 1(1P36.32) WILD-TYPE	84	54	93	68

Figure S273. Get High-res Image Gene #33: 'del_1p36.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.23' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00051

Table S274. Gene #34: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 2(1P36.23) MUTATED	151	197	0
DEL PEAK 2(1P36.23) WILD-TYPE	382	345	15

Figure S274. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p36.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S275. Gene #34: 'del_1p36.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 2(1P36.23) MUTATED	52	12	18	164
DEL PEAK 2(1P36.23) WILD-TYPE	132	225	46	1

Figure S275. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p36.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.022

Table S276. Gene #34: 'del_1p36.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 2(1P36.23) MUTATED	80	86	75
DEL PEAK 2(1P36.23) WILD-TYPE	154	168	83

Figure S276. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p36.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S277. Gene #34: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 2(1P36.23) MUTATED	55	85	108
DEL PEAK 2(1P36.23) WILD-TYPE	178	150	84

Figure S277. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p36.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S278. Gene #34: 'del_1p36.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 2(1P36.23) MUTATED	50	17	181
DEL PEAK 2(1P36.23) WILD-TYPE	153	173	86

Figure S278. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S279. Gene #34: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 2(1P36.23) MUTATED	35	15	94	68
DEL PEAK 2(1P36.23) WILD-TYPE	102	92	89	14

Figure S279. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p36.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S280. Gene #34: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 2(1P36.23) MUTATED	85	103	24
DEL PEAK 2(1P36.23) WILD-TYPE	137	81	79

Figure S280. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S281. Gene #34: 'del_1p36.23' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 2(1P36.23) MUTATED	47	84	81
DEL PEAK 2(1P36.23) WILD-TYPE	138	77	78

Figure S281. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p36.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S282. Gene #34: 'del_1p36.23' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 2(1P36.23) MUTATED	7	84	97	24
DEL PEAK 2(1P36.23) WILD-TYPE	84	53	91	65

Figure S282. Get High-res Image Gene #34: 'del_1p36.23' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S283. Gene #35: 'del_1p32.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 3(1P32.3) MUTATED	66	190	1
DEL PEAK 3(1P32.3) WILD-TYPE	467	352	14

Figure S283. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p32.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S284. Gene #35: 'del_1p32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 3(1P32.3) MUTATED	23	5	16	164
DEL PEAK 3(1P32.3) WILD-TYPE	161	232	48	1

Figure S284. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p32.3' versus 'RPPA_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.0054

Table S285. Gene #35: 'del_1p32.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 3(1P32.3) MUTATED	58	78	52
DEL PEAK 3(1P32.3) WILD-TYPE	166	126	166

Figure S285. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p32.3' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S286. Gene #35: 'del_1p32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 3(1P32.3) MUTATED	59	60	69
DEL PEAK 3(1P32.3) WILD-TYPE	175	194	89

Figure S286. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p32.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S287. Gene #35: 'del_1p32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 3(1P32.3) MUTATED	36	82	101
DEL PEAK 3(1P32.3) WILD-TYPE	197	153	91

Figure S287. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S288. Gene #35: 'del_1p32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 3(1P32.3) MUTATED	33	13	173
DEL PEAK 3(1P32.3) WILD-TYPE	170	177	94

Figure S288. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S289. Gene #35: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 3(1P32.3) MUTATED	33	10	86	67
DEL PEAK 3(1P32.3) WILD-TYPE	104	97	97	15

Figure S289. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S290. Gene #35: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 3(1P32.3) MUTATED	82	96	18
DEL PEAK 3(1P32.3) WILD-TYPE	140	88	85

Figure S290. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S291. Gene #35: 'del_1p32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 3(1P32.3) MUTATED	39	82	75
DEL PEAK 3(1P32.3) WILD-TYPE	146	79	84

Figure S291. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S292. Gene #35: 'del_1p32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 3(1P32.3) MUTATED	7	82	90	17
DEL PEAK 3(1P32.3) WILD-TYPE	84	55	98	72

Figure S292. Get High-res Image Gene #35: 'del_1p32.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p22.1' versus 'MIR_CHIERARCHICAL'

P value = 0.0049 (Fisher's exact test), Q value = 0.011

Table S293. Gene #36: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 4(1P22.1) MUTATED	25	3	17
DEL PEAK 4(1P22.1) WILD-TYPE	268	121	112

Figure S293. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S294. Gene #36: 'del_1p22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 4(1P22.1) MUTATED	46	188	0
DEL PEAK 4(1P22.1) WILD-TYPE	487	354	15

Figure S294. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S295. Gene #36: 'del_1p22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 4(1P22.1) MUTATED	12	6	14	164
DEL PEAK 4(1P22.1) WILD-TYPE	172	231	50	1

Figure S295. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1p22.1' versus 'RPPA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.04

Table S296. Gene #36: 'del_1p22.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 4(1P22.1) MUTATED	59	71	50
DEL PEAK 4(1P22.1) WILD-TYPE	165	133	168

Figure S296. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_1p22.1' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S297. Gene #36: 'del_1p22.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 4(1P22.1) MUTATED	56	58	66
DEL PEAK 4(1P22.1) WILD-TYPE	178	196	92

Figure S297. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S298. Gene #36: 'del_1p22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 4(1P22.1) MUTATED	15	81	100
DEL PEAK 4(1P22.1) WILD-TYPE	218	154	92

Figure S298. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S299. Gene #36: 'del_1p22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 4(1P22.1) MUTATED	11	11	174
DEL PEAK 4(1P22.1) WILD-TYPE	192	179	93

Figure S299. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S300. Gene #36: 'del_1p22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 4(1P22.1) MUTATED	25	9	85	67
DEL PEAK 4(1P22.1) WILD-TYPE	112	98	98	15

Figure S300. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S301. Gene #36: 'del_1p22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 4(1P22.1) MUTATED	81	98	7
DEL PEAK 4(1P22.1) WILD-TYPE	141	86	96

Figure S301. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S302. Gene #36: 'del_1p22.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 4(1P22.1) MUTATED	30	83	73
DEL PEAK 4(1P22.1) WILD-TYPE	155	78	86

Figure S302. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_1p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S303. Gene #36: 'del_1p22.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 4(1P22.1) MUTATED	7	82	90	7
DEL PEAK 4(1P22.1) WILD-TYPE	84	55	98	82

Figure S303. Get High-res Image Gene #36: 'del_1p22.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q42.11' versus 'CN_CNMF'

P value = 0.00958 (Fisher's exact test), Q value = 0.019

Table S304. Gene #37: 'del_1q42.11' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 5(1Q42.11) MUTATED	52	27	1
DEL PEAK 5(1Q42.11) WILD-TYPE	481	515	14

Figure S304. Get High-res Image Gene #37: 'del_1q42.11' versus Molecular Subtype #5: 'CN_CNMF'

'del_1q42.11' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00053

Table S305. Gene #37: 'del_1q42.11' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 5(1Q42.11) MUTATED	18	18	8	1
DEL PEAK 5(1Q42.11) WILD-TYPE	166	219	56	164

Figure S305. Get High-res Image Gene #37: 'del_1q42.11' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1q42.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.052

Table S306. Gene #37: 'del_1q42.11' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 5(1Q42.11) MUTATED	15	17	9
DEL PEAK 5(1Q42.11) WILD-TYPE	188	173	258

Figure S306. Get High-res Image Gene #37: 'del_1q42.11' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1q42.11' versus 'MIRSEQ_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.024

Table S307. Gene #37: 'del_1q42.11' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 5(1Q42.11) MUTATED	6	13	9	1
DEL PEAK 5(1Q42.11) WILD-TYPE	131	94	174	81

Figure S307. Get High-res Image Gene #37: 'del_1q42.11' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_1q42.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.05

Table S308. Gene #37: 'del_1q42.11' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 5(1Q42.11) MUTATED	7	7	5	10
DEL PEAK 5(1Q42.11) WILD-TYPE	84	130	183	79

Figure S308. Get High-res Image Gene #37: 'del_1q42.11' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00046

Table S309. Gene #38: 'del_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 6(1Q44) MUTATED	11	28	7	2
DEL PEAK 6(1Q44) WILD-TYPE	173	209	57	163

Figure S309. Get High-res Image Gene #38: 'del_1q44' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_1q44' versus 'RPPA_CHIERARCHICAL'

P value = 0.0269 (Fisher's exact test), Q value = 0.048

Table S310. Gene #38: 'del_1q44' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 6(1Q44) MUTATED	27	13	10
DEL PEAK 6(1Q44) WILD-TYPE	207	241	148

Figure S310. Get High-res Image Gene #38: 'del_1q44' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00454 (Fisher's exact test), Q value = 0.01

Table S311. Gene #38: 'del_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 6(1Q44) MUTATED	12	23	11
DEL PEAK 6(1Q44) WILD-TYPE	191	167	256

Figure S311. Get High-res Image Gene #38: 'del_1q44' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.08

Table S312. Gene #38: 'del_1q44' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 6(1Q44) MUTATED	9	14	9	3
DEL PEAK 6(1Q44) WILD-TYPE	128	93	174	79

Figure S312. Get High-res Image Gene #38: 'del_1q44' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.012

Table S313. Gene #39: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 7(2Q22.1) MUTATED	9	17	8	7
DEL PEAK 7(2Q22.1) WILD-TYPE	138	79	144	106

Figure S313. Get High-res Image Gene #39: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.051

Table S314. Gene #39: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 7(2Q22.1) MUTATED	9	16	5	11
DEL PEAK 7(2Q22.1) WILD-TYPE	139	86	95	147

Figure S314. Get High-res Image Gene #39: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.066

Table S315. Gene #39: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 7(2Q22.1) MUTATED	41	25	2
DEL PEAK 7(2Q22.1) WILD-TYPE	492	517	13

Figure S315. Get High-res Image Gene #39: 'del_2q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.076

Table S316. Gene #39: 'del_2q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 7(2Q22.1) MUTATED	15	15	3	3
DEL PEAK 7(2Q22.1) WILD-TYPE	169	222	61	162

Figure S316. Get High-res Image Gene #39: 'del_2q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.012

Table S317. Gene #40: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 8(2Q37.1) MUTATED	10	20	7	12
DEL PEAK 8(2Q37.1) WILD-TYPE	138	82	93	146

Figure S317. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.1' versus 'CN_CNMF'

P value = 0.00491 (Fisher's exact test), Q value = 0.011

Table S318. Gene #40: 'del_2q37.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 8(2Q37.1) MUTATED	45	72	4
DEL PEAK 8(2Q37.1) WILD-TYPE	488	470	11

Figure S318. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S319. Gene #40: 'del_2q37.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 8(2Q37.1) MUTATED	17	56	4	4
DEL PEAK 8(2Q37.1) WILD-TYPE	167	181	60	161

Figure S319. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_2q37.1' versus 'RPPA_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.023

Table S320. Gene #40: 'del_2q37.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 8(2Q37.1) MUTATED	25	14	35
DEL PEAK 8(2Q37.1) WILD-TYPE	199	190	183

Figure S320. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_2q37.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0058 (Fisher's exact test), Q value = 0.012

Table S321. Gene #40: 'del_2q37.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 8(2Q37.1) MUTATED	35	31	8
DEL PEAK 8(2Q37.1) WILD-TYPE	199	223	150

Figure S321. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.043

Table S322. Gene #40: 'del_2q37.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 8(2Q37.1) MUTATED	26	37	14
DEL PEAK 8(2Q37.1) WILD-TYPE	207	198	178

Figure S322. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S323. Gene #40: 'del_2q37.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 8(2Q37.1) MUTATED	15	46	16
DEL PEAK 8(2Q37.1) WILD-TYPE	188	144	251

Figure S323. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.003

Table S324. Gene #40: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 8(2Q37.1) MUTATED	25	21	13	6
DEL PEAK 8(2Q37.1) WILD-TYPE	112	86	170	76

Figure S324. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.04

Table S325. Gene #40: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 8(2Q37.1) MUTATED	33	14	18
DEL PEAK 8(2Q37.1) WILD-TYPE	189	170	85

Figure S325. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0028

Table S326. Gene #40: 'del_2q37.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 8(2Q37.1) MUTATED	37	14	13
DEL PEAK 8(2Q37.1) WILD-TYPE	148	147	146

Figure S326. Get High-res Image Gene #40: 'del_2q37.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0025

Table S327. Gene #41: 'del_3p21.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 9(3P21.31) MUTATED	15	36	6	6
DEL PEAK 9(3P21.31) WILD-TYPE	169	201	58	159

Figure S327. Get High-res Image Gene #41: 'del_3p21.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0024

Table S328. Gene #41: 'del_3p21.31' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 9(3P21.31) MUTATED	18	12	36
DEL PEAK 9(3P21.31) WILD-TYPE	206	192	182

Figure S328. Get High-res Image Gene #41: 'del_3p21.31' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.065

Table S329. Gene #41: 'del_3p21.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 9(3P21.31) MUTATED	33	23	10
DEL PEAK 9(3P21.31) WILD-TYPE	201	231	148

Figure S329. Get High-res Image Gene #41: 'del_3p21.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.045

Table S330. Gene #41: 'del_3p21.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 9(3P21.31) MUTATED	23	26	17
DEL PEAK 9(3P21.31) WILD-TYPE	180	164	250

Figure S330. Get High-res Image Gene #41: 'del_3p21.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0034

Table S331. Gene #41: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 9(3P21.31) MUTATED	13	21	9	8
DEL PEAK 9(3P21.31) WILD-TYPE	124	86	174	74

Figure S331. Get High-res Image Gene #41: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00249 (Fisher's exact test), Q value = 0.0058

Table S332. Gene #41: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 9(3P21.31) MUTATED	24	9	18
DEL PEAK 9(3P21.31) WILD-TYPE	198	175	85

Figure S332. Get High-res Image Gene #41: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00295 (Fisher's exact test), Q value = 0.0068

Table S333. Gene #42: 'del_3q13.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 10(3Q13.31) MUTATED	12	28	6	4
DEL PEAK 10(3Q13.31) WILD-TYPE	172	209	58	161

Figure S333. Get High-res Image Gene #42: 'del_3q13.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0198 (Fisher's exact test), Q value = 0.037

Table S334. Gene #42: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 10(3Q13.31) MUTATED	31	16	11
DEL PEAK 10(3Q13.31) WILD-TYPE	203	238	147

Figure S334. Get High-res Image Gene #42: 'del_3q13.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.077

Table S335. Gene #42: 'del_3q13.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 10(3Q13.31) MUTATED	15	21	13
DEL PEAK 10(3Q13.31) WILD-TYPE	188	169	254

Figure S335. Get High-res Image Gene #42: 'del_3q13.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0015

Table S336. Gene #42: 'del_3q13.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 10(3Q13.31) MUTATED	16	6	17
DEL PEAK 10(3Q13.31) WILD-TYPE	206	178	86

Figure S336. Get High-res Image Gene #42: 'del_3q13.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_3q29' versus 'METHLYATION_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.0057

Table S337. Gene #43: 'del_3q29' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 11(3Q29) MUTATED	17	32	6	5
DEL PEAK 11(3Q29) WILD-TYPE	167	205	58	160

Figure S337. Get High-res Image Gene #43: 'del_3q29' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_3q29' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00503 (Fisher's exact test), Q value = 0.011

Table S338. Gene #43: 'del_3q29' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 11(3Q29) MUTATED	25	26	15
DEL PEAK 11(3Q29) WILD-TYPE	178	164	252

Figure S338. Get High-res Image Gene #43: 'del_3q29' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_3q29' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.072

Table S339. Gene #43: 'del_3q29' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 11(3Q29) MUTATED	18	12	16
DEL PEAK 11(3Q29) WILD-TYPE	204	172	87

Figure S339. Get High-res Image Gene #43: 'del_3q29' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00523 (Fisher's exact test), Q value = 0.011

Table S340. Gene #44: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 12(4Q34.3) MUTATED	16	25	18	22
DEL PEAK 12(4Q34.3) WILD-TYPE	131	71	134	91

Figure S340. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00084

Table S341. Gene #44: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 12(4Q34.3) MUTATED	17	31	10	23
DEL PEAK 12(4Q34.3) WILD-TYPE	131	71	90	135

Figure S341. Get High-res Image Gene #44: '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 = 3.8e-05

Table S342. Gene #44: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 12(4Q34.3) MUTATED	77	151	3
DEL PEAK 12(4Q34.3) WILD-TYPE	456	391	12

Figure S342. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S343. Gene #44: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 12(4Q34.3) MUTATED	25	80	6	51
DEL PEAK 12(4Q34.3) WILD-TYPE	159	157	58	114

Figure S343. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0046

Table S344. Gene #44: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 12(4Q34.3) MUTATED	41	73	54
DEL PEAK 12(4Q34.3) WILD-TYPE	192	162	138

Figure S344. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00064

Table S345. Gene #44: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 12(4Q34.3) MUTATED	31	56	81
DEL PEAK 12(4Q34.3) WILD-TYPE	172	134	186

Figure S345. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.053

Table S346. Gene #44: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 12(4Q34.3) MUTATED	25	31	52	29
DEL PEAK 12(4Q34.3) WILD-TYPE	112	76	131	53

Figure S346. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0378 (Fisher's exact test), Q value = 0.065

Table S347. Gene #44: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 12(4Q34.3) MUTATED	62	57	18
DEL PEAK 12(4Q34.3) WILD-TYPE	160	127	85

Figure S347. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0027

Table S348. Gene #44: 'del_4q34.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 12(4Q34.3) MUTATED	33	55	49
DEL PEAK 12(4Q34.3) WILD-TYPE	152	106	110

Figure S348. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.012

Table S349. Gene #44: 'del_4q34.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 12(4Q34.3) MUTATED	24	46	55	12
DEL PEAK 12(4Q34.3) WILD-TYPE	67	91	133	77

Figure S349. Get High-res Image Gene #44: 'del_4q34.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5p15.33' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S350. Gene #45: 'del_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 13(5P15.33) MUTATED	5	22	10	14
DEL PEAK 13(5P15.33) WILD-TYPE	142	74	142	99

Figure S350. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S351. Gene #45: 'del_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 13(5P15.33) MUTATED	7	24	8	12
DEL PEAK 13(5P15.33) WILD-TYPE	141	78	92	146

Figure S351. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5p15.33' versus 'MIR_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0035

Table S352. Gene #45: 'del_5p15.33' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 13(5P15.33) MUTATED	6	28	10	7
DEL PEAK 13(5P15.33) WILD-TYPE	150	155	77	113

Figure S352. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5p15.33' versus 'CN_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.013

Table S353. Gene #45: 'del_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 13(5P15.33) MUTATED	40	63	4
DEL PEAK 13(5P15.33) WILD-TYPE	493	479	11

Figure S353. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #5: 'CN_CNMF'

'del_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S354. Gene #45: 'del_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 13(5P15.33) MUTATED	16	41	3	3
DEL PEAK 13(5P15.33) WILD-TYPE	168	196	61	162

Figure S354. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00296 (Fisher's exact test), Q value = 0.0068

Table S355. Gene #45: 'del_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 13(5P15.33) MUTATED	20	31	17
DEL PEAK 13(5P15.33) WILD-TYPE	183	159	250

Figure S355. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5p15.33' versus 'MIRSEQ_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0049

Table S356. Gene #45: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 13(5P15.33) MUTATED	11	20	17	2
DEL PEAK 13(5P15.33) WILD-TYPE	126	87	166	80

Figure S356. Get High-res Image Gene #45: 'del_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_5q34' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S357. Gene #46: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 14(5Q34) MUTATED	8	26	12	17
DEL PEAK 14(5Q34) WILD-TYPE	139	70	140	96

Figure S357. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S358. Gene #46: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 14(5Q34) MUTATED	10	31	11	11
DEL PEAK 14(5Q34) WILD-TYPE	138	71	89	147

Figure S358. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q34' versus 'MIR_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S359. Gene #46: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 14(5Q34) MUTATED	6	36	9	11
DEL PEAK 14(5Q34) WILD-TYPE	150	147	78	109

Figure S359. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #3: 'MIR_CNMF'

'del_5q34' versus 'MIR_CHIERARCHICAL'

P value = 0.00579 (Fisher's exact test), Q value = 0.012

Table S360. Gene #46: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 14(5Q34) MUTATED	42	5	15
DEL PEAK 14(5Q34) WILD-TYPE	251	119	114

Figure S360. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_5q34' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00037

Table S361. Gene #46: 'del_5q34' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 14(5Q34) MUTATED	45	83	5
DEL PEAK 14(5Q34) WILD-TYPE	488	459	10

Figure S361. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #5: 'CN_CNMF'

'del_5q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S362. Gene #46: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 14(5Q34) MUTATED	19	55	4	2
DEL PEAK 14(5Q34) WILD-TYPE	165	182	60	163

Figure S362. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_5q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S363. Gene #46: 'del_5q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 14(5Q34) MUTATED	24	46	18
DEL PEAK 14(5Q34) WILD-TYPE	179	144	249

Figure S363. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_5q34' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00037

Table S364. Gene #46: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 14(5Q34) MUTATED	15	27	18	3
DEL PEAK 14(5Q34) WILD-TYPE	122	80	165	79

Figure S364. Get High-res Image Gene #46: 'del_5q34' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'CN_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.039

Table S365. Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 15(6P25.3) MUTATED	82	54	2
DEL PEAK 15(6P25.3) WILD-TYPE	451	488	13

Figure S365. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 0.00781 (Fisher's exact test), Q value = 0.016

Table S366. Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 15(6P25.3) MUTATED	23	28	12	8
DEL PEAK 15(6P25.3) WILD-TYPE	161	209	52	157

Figure S366. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.026

Table S367. Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 15(6P25.3) MUTATED	42	23	19
DEL PEAK 15(6P25.3) WILD-TYPE	192	231	139

Figure S367. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.0046

Table S368. Gene #47: 'del_6p25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 15(6P25.3) MUTATED	42	23	14
DEL PEAK 15(6P25.3) WILD-TYPE	191	212	178

Figure S368. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0035

Table S369. Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 15(6P25.3) MUTATED	37	23	19
DEL PEAK 15(6P25.3) WILD-TYPE	166	167	248

Figure S369. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S370. Gene #48: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 16(6Q22.31) MUTATED	155	79	2
DEL PEAK 16(6Q22.31) WILD-TYPE	378	463	13

Figure S370. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q22.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S371. Gene #48: 'del_6q22.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 16(6Q22.31) MUTATED	44	49	15	8
DEL PEAK 16(6Q22.31) WILD-TYPE	140	188	49	157

Figure S371. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q22.31' versus 'RPPA_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.008

Table S372. Gene #48: 'del_6q22.31' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 16(6Q22.31) MUTATED	51	24	49
DEL PEAK 16(6Q22.31) WILD-TYPE	173	180	169

Figure S372. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q22.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00188 (Fisher's exact test), Q value = 0.0045

Table S373. Gene #48: 'del_6q22.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 16(6Q22.31) MUTATED	58	49	17
DEL PEAK 16(6Q22.31) WILD-TYPE	176	205	141

Figure S373. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6q22.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S374. Gene #48: 'del_6q22.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 16(6Q22.31) MUTATED	72	39	20
DEL PEAK 16(6Q22.31) WILD-TYPE	161	196	172

Figure S374. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q22.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S375. Gene #48: 'del_6q22.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 16(6Q22.31) MUTATED	66	39	26
DEL PEAK 16(6Q22.31) WILD-TYPE	137	151	241

Figure S375. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q22.31' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0018

Table S376. Gene #48: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 16(6Q22.31) MUTATED	34	18	19	6
DEL PEAK 16(6Q22.31) WILD-TYPE	103	89	164	76

Figure S376. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.012

Table S377. Gene #48: 'del_6q22.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 16(6Q22.31) MUTATED	40	18	17
DEL PEAK 16(6Q22.31) WILD-TYPE	145	143	142

Figure S377. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_6q22.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S378. Gene #48: 'del_6q22.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 16(6Q22.31) MUTATED	24	11	18	22
DEL PEAK 16(6Q22.31) WILD-TYPE	67	126	170	67

Figure S378. Get High-res Image Gene #48: 'del_6q22.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S379. Gene #49: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 17(6Q26) MUTATED	176	83	2
DEL PEAK 17(6Q26) WILD-TYPE	357	459	13

Figure S379. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #5: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S380. Gene #49: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 17(6Q26) MUTATED	52	51	14	8
DEL PEAK 17(6Q26) WILD-TYPE	132	186	50	157

Figure S380. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00043

Table S381. Gene #49: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 17(6Q26) MUTATED	62	25	56
DEL PEAK 17(6Q26) WILD-TYPE	162	179	162

Figure S381. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 2e-04

Table S382. Gene #49: 'del_6q26' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 17(6Q26) MUTATED	66	61	16
DEL PEAK 17(6Q26) WILD-TYPE	168	193	142

Figure S382. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S383. Gene #49: 'del_6q26' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 17(6Q26) MUTATED	75	43	20
DEL PEAK 17(6Q26) WILD-TYPE	158	192	172

Figure S383. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S384. Gene #49: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 17(6Q26) MUTATED	69	43	26
DEL PEAK 17(6Q26) WILD-TYPE	134	147	241

Figure S384. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S385. Gene #49: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 17(6Q26) MUTATED	39	17	20	5
DEL PEAK 17(6Q26) WILD-TYPE	98	90	163	77

Figure S385. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0084

Table S386. Gene #49: 'del_6q26' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 17(6Q26) MUTATED	42	18	18
DEL PEAK 17(6Q26) WILD-TYPE	143	143	141

Figure S386. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S387. Gene #49: 'del_6q26' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 17(6Q26) MUTATED	27	11	19	21
DEL PEAK 17(6Q26) WILD-TYPE	64	126	169	68

Figure S387. Get High-res Image Gene #49: 'del_6q26' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S388. Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 18(8P23.2) MUTATED	64	24	0
DEL PEAK 18(8P23.2) WILD-TYPE	469	518	15

Figure S388. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S389. Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 18(8P23.2) MUTATED	23	11	1	0
DEL PEAK 18(8P23.2) WILD-TYPE	161	226	63	165

Figure S389. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00051

Table S390. Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 18(8P23.2) MUTATED	25	5	6
DEL PEAK 18(8P23.2) WILD-TYPE	208	230	186

Figure S390. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00075

Table S391. Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 18(8P23.2) MUTATED	22	8	6
DEL PEAK 18(8P23.2) WILD-TYPE	181	182	261

Figure S391. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00765 (Fisher's exact test), Q value = 0.016

Table S392. Gene #50: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 18(8P23.2) MUTATED	9	3	10
DEL PEAK 18(8P23.2) WILD-TYPE	213	181	93

Figure S392. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0034

Table S393. Gene #50: 'del_8p23.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 18(8P23.2) MUTATED	1	7	3	10
DEL PEAK 18(8P23.2) WILD-TYPE	90	130	185	79

Figure S393. Get High-res Image Gene #50: 'del_8p23.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8q24.3' versus 'MIR_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.0077

Table S394. Gene #51: 'del_8q24.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 19(8Q24.3) MUTATED	25	14	8	4
DEL PEAK 19(8Q24.3) WILD-TYPE	131	169	79	116

Figure S394. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_8q24.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S395. Gene #51: 'del_8q24.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 19(8Q24.3) MUTATED	57	21	0
DEL PEAK 19(8Q24.3) WILD-TYPE	476	521	15

Figure S395. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_8q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S396. Gene #51: 'del_8q24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 19(8Q24.3) MUTATED	20	17	1	0
DEL PEAK 19(8Q24.3) WILD-TYPE	164	220	63	165

Figure S396. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_8q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0238 (Fisher's exact test), Q value = 0.043

Table S397. Gene #51: 'del_8q24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 19(8Q24.3) MUTATED	22	10	7
DEL PEAK 19(8Q24.3) WILD-TYPE	211	225	185

Figure S397. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_8q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.0081

Table S398. Gene #51: 'del_8q24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 19(8Q24.3) MUTATED	20	12	7
DEL PEAK 19(8Q24.3) WILD-TYPE	183	178	260

Figure S398. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00496 (Fisher's exact test), Q value = 0.011

Table S399. Gene #51: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 19(8Q24.3) MUTATED	12	9	6	0
DEL PEAK 19(8Q24.3) WILD-TYPE	125	98	177	82

Figure S399. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_8q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0034

Table S400. Gene #51: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 19(8Q24.3) MUTATED	10	4	13
DEL PEAK 19(8Q24.3) WILD-TYPE	212	180	90

Figure S400. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_8q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.041

Table S401. Gene #51: 'del_8q24.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 19(8Q24.3) MUTATED	7	6	4	9
DEL PEAK 19(8Q24.3) WILD-TYPE	84	131	184	80

Figure S401. Get High-res Image Gene #51: 'del_8q24.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S402. Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 20(9P21.3) MUTATED	100	59	132	75
DEL PEAK 20(9P21.3) WILD-TYPE	47	37	20	38

Figure S402. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S403. Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 20(9P21.3) MUTATED	101	60	91	114
DEL PEAK 20(9P21.3) WILD-TYPE	47	42	9	44

Figure S403. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'MIR_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.033

Table S404. Gene #52: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 20(9P21.3) MUTATED	196	96	101
DEL PEAK 20(9P21.3) WILD-TYPE	97	28	28

Figure S404. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S405. Gene #52: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 20(9P21.3) MUTATED	406	181	6
DEL PEAK 20(9P21.3) WILD-TYPE	127	361	9

Figure S405. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S406. Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 20(9P21.3) MUTATED	142	93	20	28
DEL PEAK 20(9P21.3) WILD-TYPE	42	144	44	137

Figure S406. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S407. Gene #52: 'del_9p21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 20(9P21.3) MUTATED	113	73	135
DEL PEAK 20(9P21.3) WILD-TYPE	111	131	83

Figure S407. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S408. Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 20(9P21.3) MUTATED	142	127	52
DEL PEAK 20(9P21.3) WILD-TYPE	92	127	106

Figure S408. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S409. Gene #52: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 20(9P21.3) MUTATED	160	62	56
DEL PEAK 20(9P21.3) WILD-TYPE	73	173	136

Figure S409. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S410. Gene #52: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 20(9P21.3) MUTATED	144	65	69
DEL PEAK 20(9P21.3) WILD-TYPE	59	125	198

Figure S410. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S411. Gene #52: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 20(9P21.3) MUTATED	59	56	59
DEL PEAK 20(9P21.3) WILD-TYPE	163	128	44

Figure S411. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.003

Table S412. Gene #52: 'del_9p21.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 20(9P21.3) MUTATED	81	41	51
DEL PEAK 20(9P21.3) WILD-TYPE	104	120	108

Figure S412. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S413. Gene #52: 'del_9p21.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 20(9P21.3) MUTATED	31	28	54	60
DEL PEAK 20(9P21.3) WILD-TYPE	60	109	134	29

Figure S413. Get High-res Image Gene #52: 'del_9p21.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S414. Gene #53: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 21(10P15.3) MUTATED	129	63	134	82
DEL PEAK 21(10P15.3) WILD-TYPE	18	33	18	31

Figure S414. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p15.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S415. Gene #53: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 21(10P15.3) MUTATED	125	59	89	135
DEL PEAK 21(10P15.3) WILD-TYPE	23	43	11	23

Figure S415. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p15.3' versus 'MIR_CNMF'

P value = 0.00822 (Fisher's exact test), Q value = 0.017

Table S416. Gene #53: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 21(10P15.3) MUTATED	139	137	70	97
DEL PEAK 21(10P15.3) WILD-TYPE	17	46	17	23

Figure S416. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p15.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.008

Table S417. Gene #53: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 21(10P15.3) MUTATED	223	105	115
DEL PEAK 21(10P15.3) WILD-TYPE	70	19	14

Figure S417. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S418. Gene #53: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 21(10P15.3) MUTATED	488	52	13
DEL PEAK 21(10P15.3) WILD-TYPE	45	490	2

Figure S418. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S419. Gene #53: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 21(10P15.3) MUTATED	168	8	21	7
DEL PEAK 21(10P15.3) WILD-TYPE	16	229	43	158

Figure S419. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p15.3' versus 'RPPA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0011

Table S420. Gene #53: 'del_10p15.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 21(10P15.3) MUTATED	90	56	100
DEL PEAK 21(10P15.3) WILD-TYPE	134	148	118

Figure S420. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p15.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0017

Table S421. Gene #53: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 21(10P15.3) MUTATED	98	108	40
DEL PEAK 21(10P15.3) WILD-TYPE	136	146	118

Figure S421. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S422. Gene #53: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 21(10P15.3) MUTATED	184	4	22
DEL PEAK 21(10P15.3) WILD-TYPE	49	231	170

Figure S422. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S423. Gene #53: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 21(10P15.3) MUTATED	178	9	23
DEL PEAK 21(10P15.3) WILD-TYPE	25	181	244

Figure S423. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00029

Table S424. Gene #53: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 21(10P15.3) MUTATED	33	26	19	5
DEL PEAK 21(10P15.3) WILD-TYPE	104	81	164	77

Figure S424. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S425. Gene #53: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 21(10P15.3) MUTATED	11	13	59
DEL PEAK 21(10P15.3) WILD-TYPE	211	171	44

Figure S425. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S426. Gene #53: 'del_10p15.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 21(10P15.3) MUTATED	61	4	18
DEL PEAK 21(10P15.3) WILD-TYPE	124	157	141

Figure S426. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S427. Gene #53: 'del_10p15.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 21(10P15.3) MUTATED	4	6	10	63
DEL PEAK 21(10P15.3) WILD-TYPE	87	131	178	26

Figure S427. Get High-res Image Gene #53: 'del_10p15.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p13' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S428. Gene #54: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 22(10P13) MUTATED	131	65	135	79
DEL PEAK 22(10P13) WILD-TYPE	16	31	17	34

Figure S428. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S429. Gene #54: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 22(10P13) MUTATED	129	58	89	134
DEL PEAK 22(10P13) WILD-TYPE	19	44	11	24

Figure S429. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p13' versus 'MIR_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0058

Table S430. Gene #54: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 22(10P13) MUTATED	141	138	68	99
DEL PEAK 22(10P13) WILD-TYPE	15	45	19	21

Figure S430. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p13' versus 'MIR_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0033

Table S431. Gene #54: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 22(10P13) MUTATED	223	108	115
DEL PEAK 22(10P13) WILD-TYPE	70	16	14

Figure S431. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S432. Gene #54: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 22(10P13) MUTATED	489	51	13
DEL PEAK 22(10P13) WILD-TYPE	44	491	2

Figure S432. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S433. Gene #54: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 22(10P13) MUTATED	168	6	21	7
DEL PEAK 22(10P13) WILD-TYPE	16	231	43	158

Figure S433. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p13' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S434. Gene #54: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 22(10P13) MUTATED	92	52	99
DEL PEAK 22(10P13) WILD-TYPE	132	152	119

Figure S434. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p13' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00023

Table S435. Gene #54: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 22(10P13) MUTATED	99	108	36
DEL PEAK 22(10P13) WILD-TYPE	135	146	122

Figure S435. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S436. Gene #54: 'del_10p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 22(10P13) MUTATED	184	4	21
DEL PEAK 22(10P13) WILD-TYPE	49	231	171

Figure S436. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S437. Gene #54: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 22(10P13) MUTATED	178	9	22
DEL PEAK 22(10P13) WILD-TYPE	25	181	245

Figure S437. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p13' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S438. Gene #54: 'del_10p13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 22(10P13) MUTATED	33	26	18	5
DEL PEAK 22(10P13) WILD-TYPE	104	81	165	77

Figure S438. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S439. Gene #54: 'del_10p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 22(10P13) MUTATED	11	11	60
DEL PEAK 22(10P13) WILD-TYPE	211	173	43

Figure S439. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S440. Gene #54: 'del_10p13' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 22(10P13) MUTATED	62	3	17
DEL PEAK 22(10P13) WILD-TYPE	123	158	142

Figure S440. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S441. Gene #54: 'del_10p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 22(10P13) MUTATED	4	5	9	64
DEL PEAK 22(10P13) WILD-TYPE	87	132	179	25

Figure S441. Get High-res Image Gene #54: 'del_10p13' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S442. Gene #55: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 23(10P11.23) MUTATED	130	61	142	83
DEL PEAK 23(10P11.23) WILD-TYPE	17	35	10	30

Figure S442. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S443. Gene #55: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 23(10P11.23) MUTATED	127	60	93	136
DEL PEAK 23(10P11.23) WILD-TYPE	21	42	7	22

Figure S443. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10p11.23' versus 'MIR_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00037

Table S444. Gene #55: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 23(10P11.23) MUTATED	145	139	67	99
DEL PEAK 23(10P11.23) WILD-TYPE	11	44	20	21

Figure S444. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10p11.23' versus 'MIR_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00011

Table S445. Gene #55: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 23(10P11.23) MUTATED	223	106	121
DEL PEAK 23(10P11.23) WILD-TYPE	70	18	8

Figure S445. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S446. Gene #55: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 23(10P11.23) MUTATED	496	49	13
DEL PEAK 23(10P11.23) WILD-TYPE	37	493	2

Figure S446. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #5: 'CN_CNMF'

'del_10p11.23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S447. Gene #55: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 23(10P11.23) MUTATED	169	6	21	7
DEL PEAK 23(10P11.23) WILD-TYPE	15	231	43	158

Figure S447. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10p11.23' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0017

Table S448. Gene #55: 'del_10p11.23' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 23(10P11.23) MUTATED	91	57	99
DEL PEAK 23(10P11.23) WILD-TYPE	133	147	119

Figure S448. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00069

Table S449. Gene #55: 'del_10p11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 23(10P11.23) MUTATED	99	109	39
DEL PEAK 23(10P11.23) WILD-TYPE	135	145	119

Figure S449. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S450. Gene #55: 'del_10p11.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 23(10P11.23) MUTATED	185	3	23
DEL PEAK 23(10P11.23) WILD-TYPE	48	232	169

Figure S450. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S451. Gene #55: 'del_10p11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 23(10P11.23) MUTATED	179	8	24
DEL PEAK 23(10P11.23) WILD-TYPE	24	182	243

Figure S451. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.23' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S452. Gene #55: 'del_10p11.23' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 23(10P11.23) MUTATED	33	26	19	4
DEL PEAK 23(10P11.23) WILD-TYPE	104	81	164	78

Figure S452. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10p11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S453. Gene #55: 'del_10p11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 23(10P11.23) MUTATED	11	13	58
DEL PEAK 23(10P11.23) WILD-TYPE	211	171	45

Figure S453. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S454. Gene #55: 'del_10p11.23' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 23(10P11.23) MUTATED	60	3	19
DEL PEAK 23(10P11.23) WILD-TYPE	125	158	140

Figure S454. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10p11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S455. Gene #55: 'del_10p11.23' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 23(10P11.23) MUTATED	4	5	11	62
DEL PEAK 23(10P11.23) WILD-TYPE	87	132	177	27

Figure S455. Get High-res Image Gene #55: 'del_10p11.23' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S456. Gene #56: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 24(10Q23.31) MUTATED	136	75	147	91
DEL PEAK 24(10Q23.31) WILD-TYPE	11	21	5	22

Figure S456. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S457. Gene #56: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 24(10Q23.31) MUTATED	132	75	98	144
DEL PEAK 24(10Q23.31) WILD-TYPE	16	27	2	14

Figure S457. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'MIR_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.024

Table S458. Gene #56: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 24(10Q23.31) MUTATED	148	158	72	107
DEL PEAK 24(10Q23.31) WILD-TYPE	8	25	15	13

Figure S458. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q23.31' versus 'MIR_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.0069

Table S459. Gene #56: 'del_10q23.31' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 24(10Q23.31) MUTATED	248	115	122
DEL PEAK 24(10Q23.31) WILD-TYPE	45	9	7

Figure S459. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S460. Gene #56: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 24(10Q23.31) MUTATED	513	100	15
DEL PEAK 24(10Q23.31) WILD-TYPE	20	442	0

Figure S460. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S461. Gene #56: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 24(10Q23.31) MUTATED	175	37	21	8
DEL PEAK 24(10Q23.31) WILD-TYPE	9	200	43	157

Figure S461. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S462. Gene #56: 'del_10q23.31' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 24(10Q23.31) MUTATED	109	58	121
DEL PEAK 24(10Q23.31) WILD-TYPE	115	146	97

Figure S462. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S463. Gene #56: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 24(10Q23.31) MUTATED	123	123	42
DEL PEAK 24(10Q23.31) WILD-TYPE	111	131	116

Figure S463. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S464. Gene #56: 'del_10q23.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 24(10Q23.31) MUTATED	197	24	27
DEL PEAK 24(10Q23.31) WILD-TYPE	36	211	165

Figure S464. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S465. Gene #56: 'del_10q23.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 24(10Q23.31) MUTATED	186	32	30
DEL PEAK 24(10Q23.31) WILD-TYPE	17	158	237

Figure S465. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S466. Gene #56: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 24(10Q23.31) MUTATED	40	37	29	8
DEL PEAK 24(10Q23.31) WILD-TYPE	97	70	154	74

Figure S466. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S467. Gene #56: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 24(10Q23.31) MUTATED	24	18	72
DEL PEAK 24(10Q23.31) WILD-TYPE	198	166	31

Figure S467. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S468. Gene #56: 'del_10q23.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 24(10Q23.31) MUTATED	75	14	25
DEL PEAK 24(10Q23.31) WILD-TYPE	110	147	134

Figure S468. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S469. Gene #56: 'del_10q23.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 24(10Q23.31) MUTATED	12	11	21	70
DEL PEAK 24(10Q23.31) WILD-TYPE	79	126	167	19

Figure S469. Get High-res Image Gene #56: 'del_10q23.31' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S470. Gene #57: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 25(10Q26.3) MUTATED	136	75	148	91
DEL PEAK 25(10Q26.3) WILD-TYPE	11	21	4	22

Figure S470. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S471. Gene #57: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 25(10Q26.3) MUTATED	132	77	97	144
DEL PEAK 25(10Q26.3) WILD-TYPE	16	25	3	14

Figure S471. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'MIR_CNMF'

P value = 0.0425 (Fisher's exact test), Q value = 0.072

Table S472. Gene #57: 'del_10q26.3' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 25(10Q26.3) MUTATED	146	162	71	107
DEL PEAK 25(10Q26.3) WILD-TYPE	10	21	16	13

Figure S472. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #3: 'MIR_CNMF'

'del_10q26.3' versus 'MIR_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0038

Table S473. Gene #57: 'del_10q26.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 25(10Q26.3) MUTATED	252	109	125
DEL PEAK 25(10Q26.3) WILD-TYPE	41	15	4

Figure S473. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S474. Gene #57: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 25(10Q26.3) MUTATED	513	137	15
DEL PEAK 25(10Q26.3) WILD-TYPE	20	405	0

Figure S474. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S475. Gene #57: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 25(10Q26.3) MUTATED	175	71	23	9
DEL PEAK 25(10Q26.3) WILD-TYPE	9	166	41	156

Figure S475. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S476. Gene #57: 'del_10q26.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 25(10Q26.3) MUTATED	117	71	129
DEL PEAK 25(10Q26.3) WILD-TYPE	107	133	89

Figure S476. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S477. Gene #57: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 25(10Q26.3) MUTATED	133	133	51
DEL PEAK 25(10Q26.3) WILD-TYPE	101	121	107

Figure S477. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S478. Gene #57: 'del_10q26.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 25(10Q26.3) MUTATED	201	46	37
DEL PEAK 25(10Q26.3) WILD-TYPE	32	189	155

Figure S478. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S479. Gene #57: 'del_10q26.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 25(10Q26.3) MUTATED	185	59	40
DEL PEAK 25(10Q26.3) WILD-TYPE	18	131	227

Figure S479. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S480. Gene #57: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 25(10Q26.3) MUTATED	55	46	38	11
DEL PEAK 25(10Q26.3) WILD-TYPE	82	61	145	71

Figure S480. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S481. Gene #57: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 25(10Q26.3) MUTATED	49	28	73
DEL PEAK 25(10Q26.3) WILD-TYPE	173	156	30

Figure S481. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S482. Gene #57: 'del_10q26.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 25(10Q26.3) MUTATED	93	22	35
DEL PEAK 25(10Q26.3) WILD-TYPE	92	139	124

Figure S482. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S483. Gene #57: 'del_10q26.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 25(10Q26.3) MUTATED	28	18	32	72
DEL PEAK 25(10Q26.3) WILD-TYPE	63	119	156	17

Figure S483. Get High-res Image Gene #57: 'del_10q26.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S484. Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 26(11P15.5) MUTATED	32	42	13	31
DEL PEAK 26(11P15.5) WILD-TYPE	115	54	139	82

Figure S484. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S485. Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 26(11P15.5) MUTATED	30	48	9	31
DEL PEAK 26(11P15.5) WILD-TYPE	118	54	91	127

Figure S485. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'MIR_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0039

Table S486. Gene #58: 'del_11p15.5' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 26(11P15.5) MUTATED	84	23	18
DEL PEAK 26(11P15.5) WILD-TYPE	209	101	111

Figure S486. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0021

Table S487. Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 26(11P15.5) MUTATED	96	130	8
DEL PEAK 26(11P15.5) WILD-TYPE	437	412	7

Figure S487. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S488. Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 26(11P15.5) MUTATED	23	93	7	1
DEL PEAK 26(11P15.5) WILD-TYPE	161	144	57	164

Figure S488. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S489. Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 26(11P15.5) MUTATED	34	72	32
DEL PEAK 26(11P15.5) WILD-TYPE	169	118	235

Figure S489. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S490. Gene #58: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 26(11P15.5) MUTATED	24	39	34	8
DEL PEAK 26(11P15.5) WILD-TYPE	113	68	149	74

Figure S490. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.024

Table S491. Gene #58: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 26(11P15.5) MUTATED	43	30	32
DEL PEAK 26(11P15.5) WILD-TYPE	179	154	71

Figure S491. Get High-res Image Gene #58: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S492. Gene #59: 'del_11p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 27(11P15.1) MUTATED	28	35	8	23
DEL PEAK 27(11P15.1) WILD-TYPE	119	61	144	90

Figure S492. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S493. Gene #59: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 27(11P15.1) MUTATED	27	37	4	26
DEL PEAK 27(11P15.1) WILD-TYPE	121	65	96	132

Figure S493. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.1' versus 'CN_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0061

Table S494. Gene #59: 'del_11p15.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 27(11P15.1) MUTATED	82	86	8
DEL PEAK 27(11P15.1) WILD-TYPE	451	456	7

Figure S494. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S495. Gene #59: 'del_11p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 27(11P15.1) MUTATED	21	58	8	1
DEL PEAK 27(11P15.1) WILD-TYPE	163	179	56	164

Figure S495. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p15.1' versus 'RPPA_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.072

Table S496. Gene #59: 'del_11p15.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 27(11P15.1) MUTATED	24	26	41
DEL PEAK 27(11P15.1) WILD-TYPE	200	178	177

Figure S496. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_11p15.1' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0028

Table S497. Gene #59: 'del_11p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 27(11P15.1) MUTATED	51	31	18
DEL PEAK 27(11P15.1) WILD-TYPE	182	204	174

Figure S497. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S498. Gene #59: 'del_11p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 27(11P15.1) MUTATED	34	49	17
DEL PEAK 27(11P15.1) WILD-TYPE	169	141	250

Figure S498. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S499. Gene #59: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 27(11P15.1) MUTATED	16	32	19	5
DEL PEAK 27(11P15.1) WILD-TYPE	121	75	164	77

Figure S499. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S500. Gene #59: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 27(11P15.1) MUTATED	27	16	29
DEL PEAK 27(11P15.1) WILD-TYPE	195	168	74

Figure S500. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.058

Table S501. Gene #59: 'del_11p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 27(11P15.1) MUTATED	13	18	19	21
DEL PEAK 27(11P15.1) WILD-TYPE	78	119	169	68

Figure S501. Get High-res Image Gene #59: 'del_11p15.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S502. Gene #60: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 28(11P11.2) MUTATED	27	35	10	23
DEL PEAK 28(11P11.2) WILD-TYPE	120	61	142	90

Figure S502. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S503. Gene #60: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 28(11P11.2) MUTATED	27	36	5	27
DEL PEAK 28(11P11.2) WILD-TYPE	121	66	95	131

Figure S503. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0191 (Fisher's exact test), Q value = 0.036

Table S504. Gene #60: 'del_11p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 28(11P11.2) MUTATED	65	22	14
DEL PEAK 28(11P11.2) WILD-TYPE	228	102	115

Figure S504. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_11p11.2' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00037

Table S505. Gene #60: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 28(11P11.2) MUTATED	87	64	8
DEL PEAK 28(11P11.2) WILD-TYPE	446	478	7

Figure S505. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_11p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S506. Gene #60: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 28(11P11.2) MUTATED	24	39	7	0
DEL PEAK 28(11P11.2) WILD-TYPE	160	198	57	165

Figure S506. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_11p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S507. Gene #60: 'del_11p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 28(11P11.2) MUTATED	48	20	12
DEL PEAK 28(11P11.2) WILD-TYPE	185	215	180

Figure S507. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S508. Gene #60: 'del_11p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 28(11P11.2) MUTATED	34	35	11
DEL PEAK 28(11P11.2) WILD-TYPE	169	155	256

Figure S508. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0013

Table S509. Gene #60: 'del_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 28(11P11.2) MUTATED	11	24	15	4
DEL PEAK 28(11P11.2) WILD-TYPE	126	83	168	78

Figure S509. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S510. Gene #60: 'del_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 28(11P11.2) MUTATED	18	10	26
DEL PEAK 28(11P11.2) WILD-TYPE	204	174	77

Figure S510. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0012

Table S511. Gene #60: 'del_11p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 28(11P11.2) MUTATED	8	13	11	21
DEL PEAK 28(11P11.2) WILD-TYPE	83	124	177	68

Figure S511. Get High-res Image Gene #60: 'del_11p11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'MRNA_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.082

Table S512. Gene #61: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 29(12P13.1) MUTATED	18	17	11	18
DEL PEAK 29(12P13.1) WILD-TYPE	129	79	141	95

Figure S512. Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.026

Table S513. Gene #61: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 29(12P13.1) MUTATED	17	20	5	22
DEL PEAK 29(12P13.1) WILD-TYPE	131	82	95	136

Figure S513. Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.00721 (Fisher's exact test), Q value = 0.015

Table S514. Gene #61: 'del_12p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 29(12P13.1) MUTATED	16	29	4	5
DEL PEAK 29(12P13.1) WILD-TYPE	168	208	60	160

Figure S514. Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00182 (Fisher's exact test), Q value = 0.0044

Table S515. Gene #61: 'del_12p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 29(12P13.1) MUTATED	18	25	11
DEL PEAK 29(12P13.1) WILD-TYPE	185	165	256

Figure S515. Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0457 (Fisher's exact test), Q value = 0.076

Table S516. Gene #61: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 29(12P13.1) MUTATED	13	11	14
DEL PEAK 29(12P13.1) WILD-TYPE	209	173	89

Figure S516. Get High-res Image Gene #61: 'del_12p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_12q12' versus 'MRNA_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.026

Table S517. Gene #62: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 30(12Q12) MUTATED	18	17	11	22
DEL PEAK 30(12Q12) WILD-TYPE	129	79	141	91

Figure S517. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0016

Table S518. Gene #62: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 30(12Q12) MUTATED	19	26	6	17
DEL PEAK 30(12Q12) WILD-TYPE	129	76	94	141

Figure S518. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.011

Table S519. Gene #62: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 30(12Q12) MUTATED	57	85	5
DEL PEAK 30(12Q12) WILD-TYPE	476	457	10

Figure S519. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S520. Gene #62: 'del_12q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 30(12Q12) MUTATED	17	59	5	7
DEL PEAK 30(12Q12) WILD-TYPE	167	178	59	158

Figure S520. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00032

Table S521. Gene #62: 'del_12q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 30(12Q12) MUTATED	17	42	25
DEL PEAK 30(12Q12) WILD-TYPE	186	148	242

Figure S521. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q12' versus 'MIRSEQ_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.015

Table S522. Gene #62: 'del_12q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 30(12Q12) MUTATED	13	26	23	8
DEL PEAK 30(12Q12) WILD-TYPE	124	81	160	74

Figure S522. Get High-res Image Gene #62: 'del_12q12' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_12q15' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00051

Table S523. Gene #63: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 31(12Q15) MUTATED	21	21	7	20
DEL PEAK 31(12Q15) WILD-TYPE	126	75	145	93

Figure S523. Get High-res Image Gene #63: 'del_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.0051

Table S524. Gene #63: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 31(12Q15) MUTATED	20	22	4	23
DEL PEAK 31(12Q15) WILD-TYPE	128	80	96	135

Figure S524. Get High-res Image Gene #63: 'del_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q15' versus 'CN_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.071

Table S525. Gene #63: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 31(12Q15) MUTATED	62	75	5
DEL PEAK 31(12Q15) WILD-TYPE	471	467	10

Figure S525. Get High-res Image Gene #63: 'del_12q15' versus Molecular Subtype #5: 'CN_CNMF'

'del_12q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S526. Gene #63: 'del_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 31(12Q15) MUTATED	16	57	4	5
DEL PEAK 31(12Q15) WILD-TYPE	168	180	60	160

Figure S526. Get High-res Image Gene #63: 'del_12q15' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S527. Gene #63: 'del_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 31(12Q15) MUTATED	18	42	20
DEL PEAK 31(12Q15) WILD-TYPE	185	148	247

Figure S527. Get High-res Image Gene #63: 'del_12q15' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_12q15' versus 'MIRSEQ_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.0028

Table S528. Gene #63: 'del_12q15' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 31(12Q15) MUTATED	11	26	20	6
DEL PEAK 31(12Q15) WILD-TYPE	126	81	163	76

Figure S528. Get High-res Image Gene #63: 'del_12q15' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S529. Gene #64: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 32(13Q14.2) MUTATED	81	45	36	53
DEL PEAK 32(13Q14.2) WILD-TYPE	66	51	116	60

Figure S529. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S530. Gene #64: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 32(13Q14.2) MUTATED	68	50	21	76
DEL PEAK 32(13Q14.2) WILD-TYPE	80	52	79	82

Figure S530. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S531. Gene #64: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 32(13Q14.2) MUTATED	214	156	13
DEL PEAK 32(13Q14.2) WILD-TYPE	319	386	2

Figure S531. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00051

Table S532. Gene #64: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 32(13Q14.2) MUTATED	62	84	16	28
DEL PEAK 32(13Q14.2) WILD-TYPE	122	153	48	137

Figure S532. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S533. Gene #64: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 32(13Q14.2) MUTATED	94	67	40
DEL PEAK 32(13Q14.2) WILD-TYPE	139	168	152

Figure S533. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S534. Gene #64: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 32(13Q14.2) MUTATED	73	74	54
DEL PEAK 32(13Q14.2) WILD-TYPE	130	116	213

Figure S534. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.033

Table S535. Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 32(13Q14.2) MUTATED	38	42	40	21
DEL PEAK 32(13Q14.2) WILD-TYPE	99	65	143	61

Figure S535. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00589 (Fisher's exact test), Q value = 0.012

Table S536. Gene #64: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 32(13Q14.2) MUTATED	66	37	38
DEL PEAK 32(13Q14.2) WILD-TYPE	156	147	65

Figure S536. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S537. Gene #65: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 33(13Q22.1) MUTATED	81	40	34	50
DEL PEAK 33(13Q22.1) WILD-TYPE	66	56	118	63

Figure S537. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00046

Table S538. Gene #65: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 33(13Q22.1) MUTATED	68	45	21	71
DEL PEAK 33(13Q22.1) WILD-TYPE	80	57	79	87

Figure S538. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S539. Gene #65: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 33(13Q22.1) MUTATED	206	149	12
DEL PEAK 33(13Q22.1) WILD-TYPE	327	393	3

Figure S539. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0043

Table S540. Gene #65: 'del_13q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 33(13Q22.1) MUTATED	62	76	15	29
DEL PEAK 33(13Q22.1) WILD-TYPE	122	161	49	136

Figure S540. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 4e-04

Table S541. Gene #65: 'del_13q22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 33(13Q22.1) MUTATED	89	65	37
DEL PEAK 33(13Q22.1) WILD-TYPE	144	170	155

Figure S541. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S542. Gene #65: 'del_13q22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 33(13Q22.1) MUTATED	71	69	51
DEL PEAK 33(13Q22.1) WILD-TYPE	132	121	216

Figure S542. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.03

Table S543. Gene #65: 'del_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 33(13Q22.1) MUTATED	39	40	37	20
DEL PEAK 33(13Q22.1) WILD-TYPE	98	67	146	62

Figure S543. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.0043

Table S544. Gene #65: 'del_13q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 33(13Q22.1) MUTATED	64	34	38
DEL PEAK 33(13Q22.1) WILD-TYPE	158	150	65

Figure S544. Get High-res Image Gene #65: 'del_13q22.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S545. Gene #66: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 34(14Q13.1) MUTATED	54	39	25	43
DEL PEAK 34(14Q13.1) WILD-TYPE	93	57	127	70

Figure S545. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00046

Table S546. Gene #66: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 34(14Q13.1) MUTATED	49	42	15	55
DEL PEAK 34(14Q13.1) WILD-TYPE	99	60	85	103

Figure S546. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S547. Gene #66: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 34(14Q13.1) MUTATED	172	66	8
DEL PEAK 34(14Q13.1) WILD-TYPE	361	476	7

Figure S547. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S548. Gene #66: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 34(14Q13.1) MUTATED	63	21	14	17
DEL PEAK 34(14Q13.1) WILD-TYPE	121	216	50	148

Figure S548. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S549. Gene #66: 'del_14q13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 34(14Q13.1) MUTATED	85	18	24
DEL PEAK 34(14Q13.1) WILD-TYPE	148	217	168

Figure S549. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_14q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S550. Gene #66: 'del_14q13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 34(14Q13.1) MUTATED	78	21	28
DEL PEAK 34(14Q13.1) WILD-TYPE	125	169	239

Figure S550. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00048

Table S551. Gene #66: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 34(14Q13.1) MUTATED	22	18	27
DEL PEAK 34(14Q13.1) WILD-TYPE	200	166	76

Figure S551. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0066

Table S552. Gene #66: 'del_14q13.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 34(14Q13.1) MUTATED	37	13	17
DEL PEAK 34(14Q13.1) WILD-TYPE	148	148	142

Figure S552. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S553. Gene #66: 'del_14q13.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 34(14Q13.1) MUTATED	8	13	18	28
DEL PEAK 34(14Q13.1) WILD-TYPE	83	124	170	61

Figure S553. Get High-res Image Gene #66: 'del_14q13.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S554. Gene #67: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 35(14Q24.2) MUTATED	51	43	22	45
DEL PEAK 35(14Q24.2) WILD-TYPE	96	53	130	68

Figure S554. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S555. Gene #67: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 35(14Q24.2) MUTATED	48	46	14	53
DEL PEAK 35(14Q24.2) WILD-TYPE	100	56	86	105

Figure S555. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.2' versus 'CN_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.012

Table S556. Gene #67: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 35(14Q24.2) MUTATED	157	127	8
DEL PEAK 35(14Q24.2) WILD-TYPE	376	415	7

Figure S556. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q24.2' versus 'RPPA_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.045

Table S557. Gene #67: 'del_14q24.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 35(14Q24.2) MUTATED	60	39	66
DEL PEAK 35(14Q24.2) WILD-TYPE	164	165	152

Figure S557. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_14q24.2' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00029

Table S558. Gene #67: 'del_14q24.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 35(14Q24.2) MUTATED	85	51	37
DEL PEAK 35(14Q24.2) WILD-TYPE	148	184	155

Figure S558. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_14q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00048

Table S559. Gene #67: 'del_14q24.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 35(14Q24.2) MUTATED	73	50	50
DEL PEAK 35(14Q24.2) WILD-TYPE	130	140	217

Figure S559. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.2' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.0011

Table S560. Gene #67: 'del_14q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 35(14Q24.2) MUTATED	50	20	32	16
DEL PEAK 35(14Q24.2) WILD-TYPE	87	87	151	66

Figure S560. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_14q24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00511 (Fisher's exact test), Q value = 0.011

Table S561. Gene #67: 'del_14q24.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 35(14Q24.2) MUTATED	52	31	35
DEL PEAK 35(14Q24.2) WILD-TYPE	170	153	68

Figure S561. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.0093

Table S562. Gene #67: 'del_14q24.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 35(14Q24.2) MUTATED	56	38	24
DEL PEAK 35(14Q24.2) WILD-TYPE	129	123	135

Figure S562. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_14q24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0035

Table S563. Gene #67: 'del_14q24.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 35(14Q24.2) MUTATED	25	32	29	32
DEL PEAK 35(14Q24.2) WILD-TYPE	66	105	159	57

Figure S563. Get High-res Image Gene #67: 'del_14q24.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q31.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S564. Gene #68: 'del_14q31.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 36(14Q31.3) MUTATED	51	39	16	41
DEL PEAK 36(14Q31.3) WILD-TYPE	96	57	136	72

Figure S564. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q31.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S565. Gene #68: 'del_14q31.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 36(14Q31.3) MUTATED	47	41	10	49
DEL PEAK 36(14Q31.3) WILD-TYPE	101	61	90	109

Figure S565. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q31.3' versus 'CN_CNMF'

P value = 0.00553 (Fisher's exact test), Q value = 0.012

Table S566. Gene #68: 'del_14q31.3' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 36(14Q31.3) MUTATED	147	120	8
DEL PEAK 36(14Q31.3) WILD-TYPE	386	422	7

Figure S566. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #5: 'CN_CNMF'

'del_14q31.3' versus 'RPPA_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.058

Table S567. Gene #68: 'del_14q31.3' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 36(14Q31.3) MUTATED	57	38	64
DEL PEAK 36(14Q31.3) WILD-TYPE	167	166	154

Figure S567. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_14q31.3' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00089

Table S568. Gene #68: 'del_14q31.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 36(14Q31.3) MUTATED	80	48	37
DEL PEAK 36(14Q31.3) WILD-TYPE	153	187	155

Figure S568. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_14q31.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00094

Table S569. Gene #68: 'del_14q31.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 36(14Q31.3) MUTATED	69	48	48
DEL PEAK 36(14Q31.3) WILD-TYPE	134	142	219

Figure S569. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_14q31.3' versus 'MIRSEQ_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.0025

Table S570. Gene #68: 'del_14q31.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 36(14Q31.3) MUTATED	48	19	32	15
DEL PEAK 36(14Q31.3) WILD-TYPE	89	88	151	67

Figure S570. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_14q31.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00794 (Fisher's exact test), Q value = 0.016

Table S571. Gene #68: 'del_14q31.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 36(14Q31.3) MUTATED	49	31	34
DEL PEAK 36(14Q31.3) WILD-TYPE	173	153	69

Figure S571. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_14q31.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00716 (Fisher's exact test), Q value = 0.015

Table S572. Gene #68: 'del_14q31.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 36(14Q31.3) MUTATED	54	36	24
DEL PEAK 36(14Q31.3) WILD-TYPE	131	125	135

Figure S572. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_14q31.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.0078

Table S573. Gene #68: 'del_14q31.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 36(14Q31.3) MUTATED	24	30	29	31
DEL PEAK 36(14Q31.3) WILD-TYPE	67	107	159	58

Figure S573. Get High-res Image Gene #68: 'del_14q31.3' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q14' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S574. Gene #69: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 37(15Q14) MUTATED	35	37	23	42
DEL PEAK 37(15Q14) WILD-TYPE	112	59	129	71

Figure S574. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q14' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S575. Gene #69: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 37(15Q14) MUTATED	33	48	12	44
DEL PEAK 37(15Q14) WILD-TYPE	115	54	88	114

Figure S575. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q14' versus 'MIR_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0019

Table S576. Gene #69: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 37(15Q14) MUTATED	34	66	22	19
DEL PEAK 37(15Q14) WILD-TYPE	122	117	65	101

Figure S576. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #3: 'MIR_CNMF'

'del_15q14' versus 'MIR_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00046

Table S577. Gene #69: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 37(15Q14) MUTATED	94	15	32
DEL PEAK 37(15Q14) WILD-TYPE	199	109	97

Figure S577. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_15q14' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00023

Table S578. Gene #69: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 37(15Q14) MUTATED	130	79	5
DEL PEAK 37(15Q14) WILD-TYPE	403	463	10

Figure S578. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #5: 'CN_CNMF'

'del_15q14' versus 'METHLYATION_CNMF'

P value = 0.00192 (Fisher's exact test), Q value = 0.0046

Table S579. Gene #69: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 37(15Q14) MUTATED	37	24	3	28
DEL PEAK 37(15Q14) WILD-TYPE	147	213	61	137

Figure S579. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_15q14' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S580. Gene #69: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 37(15Q14) MUTATED	58	29	19
DEL PEAK 37(15Q14) WILD-TYPE	175	206	173

Figure S580. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_15q14' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0013

Table S581. Gene #69: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 37(15Q14) MUTATED	50	21	35
DEL PEAK 37(15Q14) WILD-TYPE	153	169	232

Figure S581. Get High-res Image Gene #69: 'del_15q14' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S582. Gene #70: 'del_16p12.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 38(16P12.2) MUTATED	87	22	5
DEL PEAK 38(16P12.2) WILD-TYPE	446	520	10

Figure S582. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_16p12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S583. Gene #70: 'del_16p12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 38(16P12.2) MUTATED	28	12	3	2
DEL PEAK 38(16P12.2) WILD-TYPE	156	225	61	163

Figure S583. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16p12.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.03

Table S584. Gene #70: 'del_16p12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 38(16P12.2) MUTATED	31	20	8
DEL PEAK 38(16P12.2) WILD-TYPE	203	234	150

Figure S584. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_16p12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S585. Gene #70: 'del_16p12.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 38(16P12.2) MUTATED	36	8	7
DEL PEAK 38(16P12.2) WILD-TYPE	197	227	185

Figure S585. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_16p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S586. Gene #70: 'del_16p12.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 38(16P12.2) MUTATED	32	8	11
DEL PEAK 38(16P12.2) WILD-TYPE	171	182	256

Figure S586. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16p12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.04

Table S587. Gene #70: 'del_16p12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 38(16P12.2) MUTATED	7	5	10
DEL PEAK 38(16P12.2) WILD-TYPE	215	179	93

Figure S587. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16p12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.012

Table S588. Gene #70: 'del_16p12.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 38(16P12.2) MUTATED	3	6	3	10
DEL PEAK 38(16P12.2) WILD-TYPE	88	131	185	79

Figure S588. Get High-res Image Gene #70: 'del_16p12.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 0.028

Table S589. Gene #71: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 39(16Q23.1) MUTATED	31	24	16	19
DEL PEAK 39(16Q23.1) WILD-TYPE	116	72	136	94

Figure S589. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S590. Gene #71: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 39(16Q23.1) MUTATED	92	31	6
DEL PEAK 39(16Q23.1) WILD-TYPE	441	511	9

Figure S590. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S591. Gene #71: 'del_16q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 39(16Q23.1) MUTATED	33	16	3	3
DEL PEAK 39(16Q23.1) WILD-TYPE	151	221	61	162

Figure S591. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0014

Table S592. Gene #71: 'del_16q23.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 39(16Q23.1) MUTATED	37	22	7
DEL PEAK 39(16Q23.1) WILD-TYPE	197	232	151

Figure S592. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S593. Gene #71: 'del_16q23.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 39(16Q23.1) MUTATED	42	11	9
DEL PEAK 39(16Q23.1) WILD-TYPE	191	224	183

Figure S593. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S594. Gene #71: 'del_16q23.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 39(16Q23.1) MUTATED	39	9	14
DEL PEAK 39(16Q23.1) WILD-TYPE	164	181	253

Figure S594. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.028

Table S595. Gene #71: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 39(16Q23.1) MUTATED	10	6	12
DEL PEAK 39(16Q23.1) WILD-TYPE	212	178	91

Figure S595. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.057

Table S596. Gene #71: 'del_16q23.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 39(16Q23.1) MUTATED	4	5	7	11
DEL PEAK 39(16Q23.1) WILD-TYPE	87	132	181	78

Figure S596. Get High-res Image Gene #71: 'del_16q23.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.1' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00069

Table S597. Gene #72: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 40(17P13.1) MUTATED	32	27	13	16
DEL PEAK 40(17P13.1) WILD-TYPE	115	69	139	97

Figure S597. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0034

Table S598. Gene #72: 'del_17p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 40(17P13.1) MUTATED	32	27	9	20
DEL PEAK 40(17P13.1) WILD-TYPE	116	75	91	138

Figure S598. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S599. Gene #72: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 40(17P13.1) MUTATED	82	29	5
DEL PEAK 40(17P13.1) WILD-TYPE	451	513	10

Figure S599. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #5: 'CN_CNMF'

'del_17p13.1' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0013

Table S600. Gene #72: 'del_17p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 40(17P13.1) MUTATED	21	10	3	2
DEL PEAK 40(17P13.1) WILD-TYPE	163	227	61	163

Figure S600. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S601. Gene #72: 'del_17p13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 40(17P13.1) MUTATED	36	8	3
DEL PEAK 40(17P13.1) WILD-TYPE	197	227	189

Figure S601. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_17p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S602. Gene #72: 'del_17p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 40(17P13.1) MUTATED	30	13	4
DEL PEAK 40(17P13.1) WILD-TYPE	173	177	263

Figure S602. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00363 (Fisher's exact test), Q value = 0.0081

Table S603. Gene #72: 'del_17p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 40(17P13.1) MUTATED	7	2	9
DEL PEAK 40(17P13.1) WILD-TYPE	215	182	94

Figure S603. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0441 (Fisher's exact test), Q value = 0.074

Table S604. Gene #72: 'del_17p13.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 40(17P13.1) MUTATED	4	3	3	7
DEL PEAK 40(17P13.1) WILD-TYPE	87	134	185	82

Figure S604. Get High-res Image Gene #72: 'del_17p13.1' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 7.3e-05

Table S605. Gene #73: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 41(17Q11.2) MUTATED	35	9	12	5
DEL PEAK 41(17Q11.2) WILD-TYPE	112	87	140	108

Figure S605. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00014

Table S606. Gene #73: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 41(17Q11.2) MUTATED	35	7	9	10
DEL PEAK 41(17Q11.2) WILD-TYPE	113	95	91	148

Figure S606. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'MIR_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0061

Table S607. Gene #73: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 41(17Q11.2) MUTATED	29	16	4	19
DEL PEAK 41(17Q11.2) WILD-TYPE	127	167	83	101

Figure S607. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #3: 'MIR_CNMF'

'del_17q11.2' versus 'MIR_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.022

Table S608. Gene #73: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 41(17Q11.2) MUTATED	26	24	18
DEL PEAK 41(17Q11.2) WILD-TYPE	267	100	111

Figure S608. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S609. Gene #73: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 41(17Q11.2) MUTATED	66	21	6
DEL PEAK 41(17Q11.2) WILD-TYPE	467	521	9

Figure S609. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #5: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00062

Table S610. Gene #73: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 41(17Q11.2) MUTATED	22	9	5	2
DEL PEAK 41(17Q11.2) WILD-TYPE	162	228	59	163

Figure S610. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0033

Table S611. Gene #73: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 41(17Q11.2) MUTATED	29	11	7
DEL PEAK 41(17Q11.2) WILD-TYPE	205	243	151

Figure S611. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S612. Gene #73: 'del_17q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 41(17Q11.2) MUTATED	29	7	4
DEL PEAK 41(17Q11.2) WILD-TYPE	204	228	188

Figure S612. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S613. Gene #73: 'del_17q11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 41(17Q11.2) MUTATED	25	11	4
DEL PEAK 41(17Q11.2) WILD-TYPE	178	179	263

Figure S613. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.013

Table S614. Gene #73: 'del_17q11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 41(17Q11.2) MUTATED	5	3	3	9
DEL PEAK 41(17Q11.2) WILD-TYPE	86	134	185	80

Figure S614. Get High-res Image Gene #73: 'del_17q11.2' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 0.0489 (Fisher's exact test), Q value = 0.081

Table S615. Gene #74: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 42(18Q23) MUTATED	19	18	11	16
DEL PEAK 42(18Q23) WILD-TYPE	128	78	141	97

Figure S615. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.036

Table S616. Gene #74: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 42(18Q23) MUTATED	22	15	4	23
DEL PEAK 42(18Q23) WILD-TYPE	126	87	96	135

Figure S616. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.01

Table S617. Gene #74: 'del_18q23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 42(18Q23) MUTATED	32	24	5	35
DEL PEAK 42(18Q23) WILD-TYPE	152	213	59	130

Figure S617. Get High-res Image Gene #74: 'del_18q23' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNA_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.01

Table S618. Gene #75: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 43(19Q13.41) MUTATED	21	23	17	29
DEL PEAK 43(19Q13.41) WILD-TYPE	126	73	135	84

Figure S618. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.41' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00017

Table S619. Gene #75: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 43(19Q13.41) MUTATED	23	34	8	25
DEL PEAK 43(19Q13.41) WILD-TYPE	125	68	92	133

Figure S619. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.41' versus 'MIR_CHIERARCHICAL'

P value = 0.0443 (Fisher's exact test), Q value = 0.074

Table S620. Gene #75: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	293	124	129
DEL PEAK 43(19Q13.41) MUTATED	62	19	15
DEL PEAK 43(19Q13.41) WILD-TYPE	231	105	114

Figure S620. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S621. Gene #75: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 43(19Q13.41) MUTATED	74	290	2
DEL PEAK 43(19Q13.41) WILD-TYPE	459	252	13

Figure S621. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S622. Gene #75: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 43(19Q13.41) MUTATED	26	81	15	165
DEL PEAK 43(19Q13.41) WILD-TYPE	158	156	49	0

Figure S622. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.41' versus 'RPPA_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.073

Table S623. Gene #75: 'del_19q13.41' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 43(19Q13.41) MUTATED	81	98	88
DEL PEAK 43(19Q13.41) WILD-TYPE	143	106	130

Figure S623. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_19q13.41' versus 'RPPA_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0033

Table S624. Gene #75: 'del_19q13.41' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 43(19Q13.41) MUTATED	87	95	85
DEL PEAK 43(19Q13.41) WILD-TYPE	147	159	73

Figure S624. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S625. Gene #75: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 43(19Q13.41) MUTATED	43	128	121
DEL PEAK 43(19Q13.41) WILD-TYPE	190	107	71

Figure S625. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S626. Gene #75: 'del_19q13.41' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 43(19Q13.41) MUTATED	24	69	199
DEL PEAK 43(19Q13.41) WILD-TYPE	179	121	68

Figure S626. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S627. Gene #75: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 43(19Q13.41) MUTATED	50	36	107	74
DEL PEAK 43(19Q13.41) WILD-TYPE	87	71	76	8

Figure S627. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S628. Gene #75: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 43(19Q13.41) MUTATED	129	118	20
DEL PEAK 43(19Q13.41) WILD-TYPE	93	66	83

Figure S628. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S629. Gene #75: 'del_19q13.41' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 43(19Q13.41) MUTATED	61	110	95
DEL PEAK 43(19Q13.41) WILD-TYPE	124	51	64

Figure S629. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S630. Gene #75: 'del_19q13.41' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 43(19Q13.41) MUTATED	32	105	113	16
DEL PEAK 43(19Q13.41) WILD-TYPE	59	32	75	73

Figure S630. Get High-res Image Gene #75: 'del_19q13.41' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S631. Gene #76: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 44(19Q13.43) MUTATED	17	23	6	29
DEL PEAK 44(19Q13.43) WILD-TYPE	130	73	146	84

Figure S631. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S632. Gene #76: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 44(19Q13.43) MUTATED	18	32	2	23
DEL PEAK 44(19Q13.43) WILD-TYPE	130	70	98	135

Figure S632. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.43' versus 'MIR_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0025

Table S633. Gene #76: 'del_19q13.43' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 44(19Q13.43) MUTATED	14	43	9	14
DEL PEAK 44(19Q13.43) WILD-TYPE	142	140	78	106

Figure S633. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #3: 'MIR_CNMF'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S634. Gene #76: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 44(19Q13.43) MUTATED	52	299	3
DEL PEAK 44(19Q13.43) WILD-TYPE	481	243	12

Figure S634. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #5: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S635. Gene #76: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 44(19Q13.43) MUTATED	21	89	15	163
DEL PEAK 44(19Q13.43) WILD-TYPE	163	148	49	2

Figure S635. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_19q13.43' versus 'RPPA_CHIERARCHICAL'

P value = 0.00792 (Fisher's exact test), Q value = 0.016

Table S636. Gene #76: 'del_19q13.43' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 44(19Q13.43) MUTATED	90	92	81
DEL PEAK 44(19Q13.43) WILD-TYPE	144	162	77

Figure S636. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S637. Gene #76: 'del_19q13.43' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 44(19Q13.43) MUTATED	39	134	120
DEL PEAK 44(19Q13.43) WILD-TYPE	194	101	72

Figure S637. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S638. Gene #76: 'del_19q13.43' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 44(19Q13.43) MUTATED	19	76	198
DEL PEAK 44(19Q13.43) WILD-TYPE	184	114	69

Figure S638. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S639. Gene #76: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 44(19Q13.43) MUTATED	55	37	102	76
DEL PEAK 44(19Q13.43) WILD-TYPE	82	70	81	6

Figure S639. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S640. Gene #76: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 44(19Q13.43) MUTATED	136	115	19
DEL PEAK 44(19Q13.43) WILD-TYPE	86	69	84

Figure S640. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S641. Gene #76: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 44(19Q13.43) MUTATED	64	113	92
DEL PEAK 44(19Q13.43) WILD-TYPE	121	48	67

Figure S641. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S642. Gene #76: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 44(19Q13.43) MUTATED	36	108	110	15
DEL PEAK 44(19Q13.43) WILD-TYPE	55	29	78	74

Figure S642. Get High-res Image Gene #76: 'del_19q13.43' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.32' versus 'MIR_CNMF'

P value = 0.0396 (Fisher's exact test), Q value = 0.068

Table S643. Gene #77: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 45(22Q13.32) MUTATED	59	82	24	41
DEL PEAK 45(22Q13.32) WILD-TYPE	97	101	63	79

Figure S643. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #3: 'MIR_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S644. Gene #77: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	533	542	15
DEL PEAK 45(22Q13.32) MUTATED	203	81	5
DEL PEAK 45(22Q13.32) WILD-TYPE	330	461	10

Figure S644. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #5: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S645. Gene #77: 'del_22q13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 45(22Q13.32) MUTATED	65	45	15	5
DEL PEAK 45(22Q13.32) WILD-TYPE	119	192	49	160

Figure S645. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S646. Gene #77: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 45(22Q13.32) MUTATED	43	31	70
DEL PEAK 45(22Q13.32) WILD-TYPE	181	173	148

Figure S646. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0052

Table S647. Gene #77: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 45(22Q13.32) MUTATED	60	64	20
DEL PEAK 45(22Q13.32) WILD-TYPE	174	190	138

Figure S647. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S648. Gene #77: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 45(22Q13.32) MUTATED	89	29	23
DEL PEAK 45(22Q13.32) WILD-TYPE	144	206	169

Figure S648. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S649. Gene #77: 'del_22q13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 45(22Q13.32) MUTATED	80	36	25
DEL PEAK 45(22Q13.32) WILD-TYPE	123	154	242

Figure S649. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 0.0216 (Fisher's exact test), Q value = 0.04

Table S650. Gene #77: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 45(22Q13.32) MUTATED	26	23	21	7
DEL PEAK 45(22Q13.32) WILD-TYPE	111	84	162	75

Figure S650. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S651. Gene #77: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	222	184	103
DEL PEAK 45(22Q13.32) MUTATED	27	18	32
DEL PEAK 45(22Q13.32) WILD-TYPE	195	166	71

Figure S651. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.0014

Table S652. Gene #77: 'del_22q13.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	185	161	159
DEL PEAK 45(22Q13.32) MUTATED	43	18	15
DEL PEAK 45(22Q13.32) WILD-TYPE	142	143	144

Figure S652. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00035

Table S653. Gene #77: 'del_22q13.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	91	137	188	89
DEL PEAK 45(22Q13.32) MUTATED	12	18	18	28
DEL PEAK 45(22Q13.32) WILD-TYPE	79	119	170	61

Figure S653. Get High-res Image Gene #77: 'del_22q13.32' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'MRNA_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.013

Table S654. Gene #78: 'del_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	147	96	152	113
DEL PEAK 46(XP22.2) MUTATED	24	32	25	27
DEL PEAK 46(XP22.2) WILD-TYPE	123	64	127	86

Figure S654. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xp22.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00145 (Fisher's exact test), Q value = 0.0036

Table S655. Gene #78: 'del_xp22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 46(XP22.2) MUTATED	22	36	18	32
DEL PEAK 46(XP22.2) WILD-TYPE	126	66	82	126

Figure S655. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.0083

Table S656. Gene #78: 'del_xp22.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 46(XP22.2) MUTATED	35	65	5	34
DEL PEAK 46(XP22.2) WILD-TYPE	149	172	59	131

Figure S656. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.0068

Table S657. Gene #78: 'del_xp22.2' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 46(XP22.2) MUTATED	49	30	62
DEL PEAK 46(XP22.2) WILD-TYPE	175	174	156

Figure S657. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.039

Table S658. Gene #78: 'del_xp22.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 46(XP22.2) MUTATED	64	52	25
DEL PEAK 46(XP22.2) WILD-TYPE	170	202	133

Figure S658. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.032

Table S659. Gene #78: 'del_xp22.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	203	190	267
DEL PEAK 46(XP22.2) MUTATED	43	57	50
DEL PEAK 46(XP22.2) WILD-TYPE	160	133	217

Figure S659. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.054

Table S660. Gene #78: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 46(XP22.2) MUTATED	27	27	30	26
DEL PEAK 46(XP22.2) WILD-TYPE	110	80	153	56

Figure S660. Get High-res Image Gene #78: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

'del_xq21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.0023

Table S661. Gene #79: 'del_xq21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	148	102	100	158
DEL PEAK 47(XQ21.1) MUTATED	16	32	16	29
DEL PEAK 47(XQ21.1) WILD-TYPE	132	70	84	129

Figure S661. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xq21.1' versus 'MIR_CNMF'

P value = 0.038 (Fisher's exact test), Q value = 0.065

Table S662. Gene #79: 'del_xq21.1' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	156	183	87	120
DEL PEAK 47(XQ21.1) MUTATED	24	46	14	16
DEL PEAK 47(XQ21.1) WILD-TYPE	132	137	73	104

Figure S662. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #3: 'MIR_CNMF'

'del_xq21.1' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.021

Table S663. Gene #79: 'del_xq21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	237	64	165
DEL PEAK 47(XQ21.1) MUTATED	40	39	3	30
DEL PEAK 47(XQ21.1) WILD-TYPE	144	198	61	135

Figure S663. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'del_xq21.1' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0017

Table S664. Gene #79: 'del_xq21.1' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	224	204	218
DEL PEAK 47(XQ21.1) MUTATED	40	21	53
DEL PEAK 47(XQ21.1) WILD-TYPE	184	183	165

Figure S664. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #7: 'RPPA_CNMF'

'del_xq21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.055

Table S665. Gene #79: 'del_xq21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	254	158
DEL PEAK 47(XQ21.1) MUTATED	52	43	19
DEL PEAK 47(XQ21.1) WILD-TYPE	182	211	139

Figure S665. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

'del_xq21.1' versus 'MRNASEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0031

Table S666. Gene #79: 'del_xq21.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	233	235	192
DEL PEAK 47(XQ21.1) MUTATED	57	38	21
DEL PEAK 47(XQ21.1) WILD-TYPE	176	197	171

Figure S666. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

'del_xq21.1' versus 'MIRSEQ_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0027

Table S667. Gene #79: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	137	107	183	82
DEL PEAK 47(XQ21.1) MUTATED	14	19	21	24
DEL PEAK 47(XQ21.1) WILD-TYPE	123	88	162	58

Figure S667. Get High-res Image Gene #79: 'del_xq21.1' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBMLGG-TP/20157420/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/GBMLGG-TP/20148947/GBMLGG-TP.transferedmergedcluster.txt
Number of patients = 1090
Number of significantly focal cnvs = 79
Number of molecular subtypes = 14
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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