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 88 focal events and 10 molecular subtypes across 441 patients, 607 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.
amp_9p13.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_10q26.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_11p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'RPPA_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq27.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q33.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q23.2 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_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 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_9p21.3 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_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 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_17q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 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_19q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 88 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 607 significant findings detected.


		Clinical Features	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
amp 1q21 3	160 (36%)	281	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0334 (0.0501)	0.00467 (0.00858)	1e-05 (3.58e-05)	0.0002 (0.000515)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00306 (0.00582)	1e-05 (3.58e-05)
amp 5p15 33	130 (29%)	311	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0351 (0.0523)	0.0371 (0.0553)	1e-05 (3.58e-05)	7e-05 (0.000199)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00241 (0.00464)	2e-05 (6.62e-05)
del 1p36 11	135 (31%)	306	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00131 (0.00274)	8e-05 (0.000225)	1e-05 (3.58e-05)	0.00023 (0.000582)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00569 (0.0103)	1e-05 (3.58e-05)
del 17p12	181 (41%)	260	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0164 (0.0267)	0.00155 (0.00318)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00174 (0.00355)	2e-05 (6.62e-05)
amp 6p21 1	124 (28%)	317	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0333 (0.0501)	0.0558 (0.0796)	1e-05 (3.58e-05)	0.00135 (0.00282)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0035 (0.00655)	2e-05 (6.62e-05)
amp 11p11 2	92 (21%)	349	1e-05 (3.58e-05)	4e-05 (0.000121)	0.717 (0.749)	0.0389 (0.0576)	0.00116 (0.00246)	0.00973 (0.0168)	5e-05 (0.000148)	1e-05 (3.58e-05)	0.0022 (0.00431)	2e-05 (6.62e-05)
amp 11q13 3	115 (26%)	326	1e-05 (3.58e-05)	0.00191 (0.00382)	0.0432 (0.063)	0.0633 (0.088)	0.00655 (0.0117)	0.0021 (0.00414)	0.00034 (0.000831)	0.00041 (0.000983)	0.00177 (0.00359)	0.00106 (0.00228)
amp 15q26 1	113 (26%)	328	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.146 (0.185)	0.0113 (0.019)	2e-05 (6.62e-05)	1e-05 (3.58e-05)	5e-05 (0.000148)	1e-05 (3.58e-05)	0.00012 (0.000321)	0.00079 (0.00175)
amp 17q12	147 (33%)	294	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00726 (0.0129)	6e-05 (0.000174)	1e-05 (3.58e-05)	5e-05 (0.000148)	1e-05 (3.58e-05)	2e-05 (6.62e-05)	0.0736 (0.1)	0.00151 (0.0031)
amp 19q12	130 (29%)	311	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00027 (0.000677)	0.00013 (0.000345)	1e-05 (3.58e-05)	4e-05 (0.000121)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0583 (0.0824)	1e-05 (3.58e-05)
amp 20q13 2	293 (66%)	148	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0276 (0.0425)	2e-05 (6.62e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0501 (0.0724)	1e-05 (3.58e-05)
del 1p13 2	93 (21%)	348	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00265 (0.00508)	0.138 (0.177)	1e-05 (3.58e-05)	0.00023 (0.000582)	0.00223 (0.00435)	0.00244 (0.00469)	0.0207 (0.0329)	0.00054 (0.00125)
del 4q35 1	204 (46%)	237	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.831 (0.847)	0.00745 (0.0131)	1e-05 (3.58e-05)	0.00038 (0.000919)	0.00012 (0.000321)	1e-05 (3.58e-05)	0.00668 (0.0119)	2e-05 (6.62e-05)
del 5q12 1	170 (39%)	271	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.136 (0.175)	0.00026 (0.000654)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00073 (0.00163)	1e-05 (3.58e-05)
del 5q23 2	158 (36%)	283	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.117 (0.153)	0.00079 (0.00175)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)
del 9p23	195 (44%)	246	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.728 (0.756)	0.00019 (0.000492)	1e-05 (3.58e-05)	3e-05 (9.5e-05)	0.00116 (0.00246)	3e-05 (9.5e-05)	0.0391 (0.0578)	0.00118 (0.0025)
del 9p21 3	193 (44%)	248	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.438 (0.485)	0.00101 (0.00218)	1e-05 (3.58e-05)	3e-05 (9.5e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0336 (0.0503)	0.00016 (0.00042)
del 10q23 31	116 (26%)	325	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0332 (0.05)	0.00797 (0.014)	1e-05 (3.58e-05)	4e-05 (0.000121)	0.00031 (0.000764)	1e-05 (3.58e-05)	0.0621 (0.0867)	0.00088 (0.00193)
del 15q11 2	120 (27%)	321	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00068 (0.00152)	0.00234 (0.00455)	2e-05 (6.62e-05)	4e-05 (0.000121)	0.00038 (0.000919)	1e-05 (3.58e-05)	0.0504 (0.0726)	0.00058 (0.00133)
del 15q15 1	122 (28%)	319	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0024 (0.00463)	0.0222 (0.0349)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00041 (0.000983)	1e-05 (3.58e-05)	0.0868 (0.117)	2e-05 (6.62e-05)
del 19p13 3	162 (37%)	279	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0547 (0.0783)	6e-05 (0.000174)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00058 (0.00133)	1e-05 (3.58e-05)
amp 1q42 3	150 (34%)	291	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.351 (0.399)	0.00235 (0.00455)	1e-05 (3.58e-05)	0.012 (0.0201)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0758 (0.103)	4e-05 (0.000121)
amp 7p22 1	229 (52%)	212	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.589 (0.629)	0.218 (0.259)	1e-05 (3.58e-05)	0.00194 (0.00387)	0.00185 (0.00373)	9e-05 (0.000251)	0.00949 (0.0164)	0.00068 (0.00152)
amp 7p11 2	214 (49%)	227	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.603 (0.643)	0.169 (0.208)	0.00088 (0.00193)	0.046 (0.0668)	0.0283 (0.0435)	0.00075 (0.00167)	0.0101 (0.0173)	0.00469 (0.0086)
amp 7q21 2	204 (46%)	237	1e-05 (3.58e-05)	6e-05 (0.000174)	0.146 (0.185)	0.119 (0.155)	0.0327 (0.0495)	0.0197 (0.0316)	0.0405 (0.0596)	0.00671 (0.012)	0.0239 (0.0374)	0.0147 (0.0243)
amp 19q13 32	111 (25%)	330	1e-05 (3.58e-05)	0.00226 (0.0044)	0.187 (0.228)	0.0114 (0.0192)	0.00038 (0.000919)	0.00335 (0.00633)	3e-05 (9.5e-05)	0.00149 (0.00307)	0.0533 (0.0764)	0.00039 (0.00094)
del 3p26 1	143 (32%)	298	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.609 (0.646)	0.0899 (0.12)	1e-05 (3.58e-05)	0.00107 (0.00229)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0201 (0.0321)	1e-05 (3.58e-05)
del 3p21 1	153 (35%)	288	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.531 (0.574)	0.14 (0.179)	0.00044 (0.00105)	0.0018 (0.00364)	0.0124 (0.0206)	7e-05 (0.000199)	0.0135 (0.0223)	0.001 (0.00217)
del 3p14 2	157 (36%)	284	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.468 (0.513)	0.0708 (0.0972)	1e-05 (3.58e-05)	6e-05 (0.000174)	0.00014 (0.00037)	1e-05 (3.58e-05)	0.00058 (0.00133)	1e-05 (3.58e-05)
del 4p16 3	169 (38%)	272	1e-05 (3.58e-05)	2e-05 (6.62e-05)	0.498 (0.543)	0.471 (0.516)	4e-05 (0.000121)	0.014 (0.0232)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00089 (0.00194)	1e-05 (3.58e-05)
del 6p25 3	115 (26%)	326	1e-05 (3.58e-05)	2e-05 (6.62e-05)	0.117 (0.153)	0.193 (0.233)	1e-05 (3.58e-05)	0.00029 (0.000717)	0.00044 (0.00105)	3e-05 (9.5e-05)	0.00195 (0.00388)	0.00371 (0.00692)
del 6q26	102 (23%)	339	1e-05 (3.58e-05)	0.00301 (0.00573)	0.395 (0.444)	0.297 (0.345)	5e-05 (0.000148)	1e-05 (3.58e-05)	0.00434 (0.00802)	0.00343 (0.00645)	0.0212 (0.0335)	0.00724 (0.0128)
del 9q21 11	113 (26%)	328	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.832 (0.848)	0.00609 (0.0109)	1e-05 (3.58e-05)	0.00235 (0.00455)	0.00018 (0.000467)	1e-05 (3.58e-05)	0.0594 (0.0835)	9e-05 (0.000251)
del 11p15 5	97 (22%)	344	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0674 (0.093)	0.00212 (0.00417)	1e-05 (3.58e-05)	0.0001 (0.000274)	0.177 (0.216)	0.00088 (0.00193)	0.0413 (0.0606)	0.0168 (0.0273)
del 14q23 3	136 (31%)	305	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.677 (0.711)	0.355 (0.403)	1e-05 (3.58e-05)	3e-05 (9.5e-05)	4e-05 (0.000121)	1e-05 (3.58e-05)	0.00376 (0.007)	6e-05 (0.000174)
del 14q32 32	133 (30%)	308	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.768 (0.792)	0.638 (0.673)	0.00676 (0.012)	0.00047 (0.0011)	0.0134 (0.0222)	0.00412 (0.00765)	0.042 (0.0615)	0.0103 (0.0176)
del 16p13 3	98 (22%)	343	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.697 (0.728)	0.485 (0.53)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.00318 (0.00603)	1e-05 (3.58e-05)
del 16q23 1	182 (41%)	259	1e-05 (3.58e-05)	0.00124 (0.0026)	0.908 (0.916)	0.153 (0.193)	0.00536 (0.00977)	8e-05 (0.000225)	0.0058 (0.0105)	0.00355 (0.00663)	0.0281 (0.0433)	0.00095 (0.00207)
del 18q12 2	181 (41%)	260	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.343 (0.392)	0.0971 (0.129)	0.0001 (0.000274)	0.0001 (0.000274)	0.0014 (0.00291)	0.00028 (7e-04)	0.00445 (0.00819)	3e-05 (9.5e-05)
del 18q21 2	204 (46%)	237	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.533 (0.576)	0.0626 (0.0873)	2e-05 (6.62e-05)	0.00013 (0.000345)	0.002 (0.00396)	0.00042 (0.001)	0.00431 (0.00798)	0.00049 (0.00114)
del 19q13 11	75 (17%)	366	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.322 (0.371)	0.687 (0.719)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0194 (0.0313)	2e-05 (6.62e-05)
del 21q11 2	182 (41%)	259	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.611 (0.648)	0.164 (0.203)	0.0001 (0.000274)	0.0027 (0.00517)	0.00187 (0.00376)	0.00058 (0.00133)	0.00087 (0.00192)	0.00057 (0.00132)
del 21q22 13	196 (44%)	245	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.158 (0.198)	0.161 (0.2)	0.00021 (0.000537)	0.00083 (0.00184)	0.00214 (0.0042)	5e-05 (0.000148)	0.00559 (0.0101)	0.00137 (0.00285)
del 22q13 31	161 (37%)	280	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.878 (0.889)	0.0102 (0.0175)	0.00105 (0.00226)	0.0012 (0.00253)	3e-05 (9.5e-05)	1e-05 (3.58e-05)	0.115 (0.151)	0.00012 (0.000321)
amp 1p36 22	66 (15%)	375	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.243 (0.286)	0.527 (0.571)	0.00017 (0.000444)	0.0109 (0.0184)	0.00335 (0.00633)	0.00046 (0.00109)	0.0567 (0.0805)	0.0289 (0.0441)
amp 5p13 1	126 (29%)	315	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.731 (0.759)	0.15 (0.19)	1e-05 (3.58e-05)	0.0002 (0.000515)	0.00011 (0.000297)	1e-05 (3.58e-05)	0.435 (0.481)	0.00011 (0.000297)
amp 6q12	88 (20%)	353	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0752 (0.102)	0.573 (0.615)	1e-05 (3.58e-05)	0.00558 (0.0101)	1e-05 (3.58e-05)	3e-05 (9.5e-05)	0.086 (0.116)	0.00011 (0.000297)
amp 6q21	82 (19%)	359	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.467 (0.513)	0.468 (0.513)	1e-05 (3.58e-05)	5e-05 (0.000148)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.171 (0.21)	1e-05 (3.58e-05)
amp 8q24 21	309 (70%)	132	0.00742 (0.0131)	1e-05 (3.58e-05)	0.201 (0.241)	0.637 (0.673)	1e-05 (3.58e-05)	0.247 (0.291)	1e-05 (3.58e-05)	0.00017 (0.000444)	0.00897 (0.0156)	0.00064 (0.00145)
amp 10p11 22	119 (27%)	322	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.925 (0.93)	0.276 (0.322)	7e-05 (0.000199)	0.09 (0.12)	0.00191 (0.00382)	1e-05 (3.58e-05)	0.0104 (0.0178)	0.00011 (0.000297)
amp 13q12 3	170 (39%)	271	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0589 (0.0832)	0.534 (0.577)	1e-05 (3.58e-05)	0.00119 (0.00251)	1e-05 (3.58e-05)	0.00011 (0.000297)	0.588 (0.628)	1e-05 (3.58e-05)
amp 13q22 1	181 (41%)	260	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.303 (0.351)	0.406 (0.455)	1e-05 (3.58e-05)	2e-05 (6.62e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.072 (0.0984)	8e-05 (0.000225)
amp 18q11 2	140 (32%)	301	1e-05 (3.58e-05)	6e-05 (0.000174)	0.926 (0.931)	0.063 (0.0877)	1e-05 (3.58e-05)	0.00108 (0.0023)	0.0158 (0.0258)	0.00029 (0.000717)	0.117 (0.153)	0.0288 (0.044)
del 3q26 31	49 (11%)	392	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.575 (0.616)	0.483 (0.528)	1e-05 (3.58e-05)	2e-05 (6.62e-05)	1e-05 (3.58e-05)	0.00029 (0.000717)	0.0616 (0.0862)	0.0132 (0.022)
del 4q22 1	193 (44%)	248	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.958 (0.96)	0.0666 (0.092)	0.00067 (0.00151)	0.0224 (0.0351)	0.00959 (0.0165)	8e-05 (0.000225)	0.67 (0.706)	0.00344 (0.00645)
del 6q24 3	78 (18%)	363	1e-05 (3.58e-05)	0.00047 (0.0011)	0.562 (0.604)	0.606 (0.645)	0.00022 (0.000561)	0.00052 (0.00121)	0.0894 (0.12)	0.0289 (0.0441)	0.02 (0.0321)	0.0377 (0.0559)
del 7q31 1	71 (16%)	370	1e-05 (3.58e-05)	0.00122 (0.00256)	0.88 (0.89)	0.371 (0.42)	0.00997 (0.0171)	0.0298 (0.0452)	0.00198 (0.00393)	0.0329 (0.0497)	0.0728 (0.0991)	0.0243 (0.038)
del 7q36 3	98 (22%)	343	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.208 (0.249)	0.0653 (0.0905)	1e-05 (3.58e-05)	3e-05 (9.5e-05)	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0501 (0.0724)	4e-05 (0.000121)
del 8p23 2	122 (28%)	319	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.061 (0.0854)	0.145 (0.184)	1e-05 (3.58e-05)	0.00023 (0.000582)	0.0196 (0.0316)	7e-05 (0.000199)	0.0748 (0.102)	0.00021 (0.000537)
del 10q22 3	79 (18%)	362	1e-05 (3.58e-05)	0.00024 (0.000605)	0.809 (0.828)	0.106 (0.14)	2e-05 (6.62e-05)	0.00063 (0.00143)	0.0157 (0.0258)	4e-05 (0.000121)	0.383 (0.431)	0.0121 (0.0202)
del 11q23 2	99 (22%)	342	1e-05 (3.58e-05)	2e-05 (6.62e-05)	0.233 (0.277)	0.0294 (0.0447)	0.00747 (0.0131)	0.00837 (0.0146)	0.516 (0.56)	0.056 (0.0798)	0.0109 (0.0184)	0.021 (0.0332)
del 12p13 1	77 (17%)	364	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.769 (0.792)	0.19 (0.231)	1e-05 (3.58e-05)	3e-05 (9.5e-05)	0.00108 (0.0023)	0.00061 (0.00139)	0.375 (0.423)	0.00018 (0.000467)
del 20p12 1	39 (9%)	402	0.00221 (0.00432)	0.00167 (0.00342)	0.358 (0.406)	0.403 (0.451)	0.0146 (0.0241)	0.0283 (0.0435)	0.0202 (0.0323)	0.0285 (0.0436)	0.971 (0.972)	0.0205 (0.0327)
amp 3q26 2	164 (37%)	277	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.0594 (0.0835)	0.0641 (0.089)	0.0221 (0.0348)	1e-05 (3.58e-05)	0.0708 (0.0972)	0.00561 (0.0102)	0.0728 (0.0991)	0.00033 (0.000809)
amp 7q22 1	202 (46%)	239	1e-05 (3.58e-05)	0.00049 (0.00114)	0.181 (0.221)	0.274 (0.32)	0.0465 (0.0674)	0.137 (0.177)	0.11 (0.144)	0.0313 (0.0473)	0.041 (0.0602)	0.0275 (0.0425)
del 2q37 2	72 (16%)	369	1e-05 (3.58e-05)	2e-05 (6.62e-05)	0.18 (0.219)	0.304 (0.352)	0.0179 (0.029)	0.109 (0.143)	6e-05 (0.000174)	7e-05 (0.000199)	0.139 (0.179)	0.00935 (0.0162)
del 6q14 1	89 (20%)	352	1e-05 (3.58e-05)	0.00013 (0.000345)	0.185 (0.224)	0.197 (0.238)	5e-05 (0.000148)	0.00016 (0.00042)	0.133 (0.172)	0.012 (0.0202)	0.0116 (0.0195)	0.359 (0.408)
amp 11p13	88 (20%)	353	1e-05 (3.58e-05)	0.00147 (0.00304)	0.806 (0.827)	0.141 (0.179)	0.129 (0.167)	0.0821 (0.111)	0.0006 (0.00137)	4e-05 (0.000121)	0.265 (0.31)	0.00107 (0.00229)
del 2q32 1	64 (15%)	377	0.00046 (0.00109)	0.00037 (0.000902)	0.835 (0.849)	0.418 (0.468)	0.0217 (0.0342)	0.581 (0.622)	0.00481 (0.0088)	0.00029 (0.000717)	0.198 (0.238)	0.159 (0.199)
del 10p15 3	77 (17%)	364	1e-05 (3.58e-05)	0.00033 (0.000809)	0.727 (0.756)	0.16 (0.2)	0.0113 (0.0191)	0.0555 (0.0793)	0.035 (0.0523)	0.00338 (0.00637)	0.14 (0.179)	0.109 (0.143)
del xp22 2	85 (19%)	356	1e-05 (3.58e-05)	3e-05 (9.5e-05)	0.721 (0.751)	0.315 (0.364)	0.0422 (0.0616)	0.399 (0.448)	0.0255 (0.0398)	0.00147 (0.00304)	0.432 (0.48)	0.152 (0.191)
amp 9p13 2	91 (21%)	350	0.04 (0.0591)	0.327 (0.375)	0.47 (0.515)	0.0442 (0.0642)	0.0376 (0.0559)	0.0593 (0.0835)	0.00599 (0.0108)	0.158 (0.198)	0.162 (0.201)	0.316 (0.364)
amp 9q34 3	122 (28%)	319	0.00177 (0.00359)	0.0207 (0.0329)	0.8 (0.821)	0.292 (0.339)	0.00743 (0.0131)	0.1 (0.133)	0.0267 (0.0414)	0.215 (0.256)	0.435 (0.481)	0.499 (0.544)
amp 14q21 3	54 (12%)	387	4e-05 (0.000121)	0.00272 (0.00519)	0.919 (0.925)	0.263 (0.308)	0.029 (0.0441)	0.143 (0.182)	0.243 (0.286)	0.45 (0.497)	0.00912 (0.0158)	0.201 (0.242)
amp xq27 3	83 (19%)	358	0.0001 (0.000274)	0.0992 (0.132)	0.865 (0.878)	0.455 (0.501)	0.0205 (0.0327)	0.0081 (0.0142)	0.00066 (0.00149)	0.672 (0.706)	0.173 (0.212)	0.347 (0.396)
del 12q12	59 (13%)	382	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.762 (0.787)	0.91 (0.918)	0.0106 (0.018)	0.0693 (0.0955)	0.327 (0.375)	0.0192 (0.0311)	0.421 (0.47)	0.0567 (0.0805)
del 17q24 3	76 (17%)	365	1e-05 (3.58e-05)	0.0001 (0.000274)	0.868 (0.88)	0.427 (0.475)	0.00177 (0.00359)	0.0504 (0.0726)	0.86 (0.874)	0.0134 (0.0222)	0.362 (0.409)	0.537 (0.579)
amp 8p23 1	177 (40%)	264	0.00064 (0.00145)	4e-05 (0.000121)	0.151 (0.191)	0.817 (0.834)	0.169 (0.208)	0.0179 (0.0291)	0.0718 (0.0982)	0.164 (0.202)	0.755 (0.781)	0.202 (0.243)
amp 10q22 2	86 (20%)	355	1e-05 (3.58e-05)	0.00205 (0.00405)	0.807 (0.827)	0.385 (0.433)	0.182 (0.222)	0.0111 (0.0189)	0.259 (0.303)	0.333 (0.381)	0.152 (0.192)	0.349 (0.397)
amp 10q26 13	88 (20%)	353	1e-05 (3.58e-05)	0.00098 (0.00213)	0.632 (0.669)	0.323 (0.372)	0.0403 (0.0594)	0.0952 (0.127)	0.13 (0.169)	0.087 (0.117)	0.451 (0.497)	0.426 (0.475)
amp 12p12 1	128 (29%)	313	1e-05 (3.58e-05)	0.0157 (0.0257)	0.124 (0.162)	0.288 (0.336)	0.239 (0.282)	0.116 (0.153)	0.14 (0.179)	0.252 (0.296)	0.0257 (0.0399)	0.0527 (0.0757)
amp 12q15	109 (25%)	332	0.00047 (0.0011)	0.00652 (0.0117)	0.0176 (0.0286)	0.207 (0.247)	0.815 (0.833)	0.308 (0.356)	0.162 (0.202)	0.095 (0.127)	0.107 (0.141)	0.176 (0.216)
del 13q12 11	63 (14%)	378	1e-05 (3.58e-05)	0.0422 (0.0616)	0.541 (0.582)	0.236 (0.28)	0.337 (0.386)	0.0197 (0.0316)	0.898 (0.907)	0.2 (0.24)	0.68 (0.712)	0.672 (0.706)
del xq21 33	57 (13%)	384	1e-05 (3.58e-05)	1e-05 (3.58e-05)	0.737 (0.764)	0.0606 (0.0851)	0.0661 (0.0915)	0.258 (0.303)	0.263 (0.308)	0.0256 (0.0399)	0.215 (0.256)	0.153 (0.192)
amp 9p24 1	65 (15%)	376	0.933 (0.936)	0.163 (0.202)	0.503 (0.547)	0.725 (0.755)	0.125 (0.162)	0.0245 (0.0383)	0.052 (0.0747)	0.361 (0.409)	0.0329 (0.0496)	0.117 (0.153)
del 1q44	25 (6%)	416	0.00858 (0.015)	0.00185 (0.00373)	0.596 (0.636)	0.138 (0.178)	0.677 (0.711)	0.159 (0.199)	0.787 (0.809)	0.746 (0.772)	0.527 (0.571)	0.203 (0.243)
del 2q33 3	49 (11%)	392	2e-05 (6.62e-05)	0.165 (0.203)	0.0713 (0.0977)	0.427 (0.475)	0.219 (0.26)	0.17 (0.209)	0.0783 (0.106)	0.0044 (0.00812)	0.606 (0.645)	0.159 (0.199)
del xp21 1	76 (17%)	365	1e-05 (3.58e-05)	0.00529 (0.00966)	0.988 (0.988)	0.776 (0.799)	0.12 (0.157)	0.634 (0.671)	0.057 (0.0808)	0.191 (0.231)	0.427 (0.475)	0.561 (0.603)

'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S1. Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 1(1P36.22) MUTATED	59	2	5	0
AMP PEAK 1(1P36.22) WILD-TYPE	175	151	46	3

Figure S1. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p36.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S2. Gene #1: 'amp_1p36.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 1(1P36.22) MUTATED	11	16	0	25	6
AMP PEAK 1(1P36.22) WILD-TYPE	34	94	51	75	81

Figure S2. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00044

Table S3. Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 1(1P36.22) MUTATED	27	5	10	14	6
AMP PEAK 1(1P36.22) WILD-TYPE	67	89	83	68	44

Figure S3. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1p36.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.018

Table S4. Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 1(1P36.22) MUTATED	22	4	24	12
AMP PEAK 1(1P36.22) WILD-TYPE	87	78	111	75

Figure S4. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.0063

Table S5. Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 1(1P36.22) MUTATED	15	8	7	9	9	17
AMP PEAK 1(1P36.22) WILD-TYPE	46	58	73	102	41	49

Figure S5. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1p36.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S6. Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 1(1P36.22) MUTATED	34	4	27
AMP PEAK 1(1P36.22) WILD-TYPE	209	78	82

Figure S6. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.044

Table S7. Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 1(1P36.22) MUTATED	15	4	4	13	13
AMP PEAK 1(1P36.22) WILD-TYPE	88	68	40	49	47

Figure S7. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S8. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 2(1Q21.3) MUTATED	130	11	18	1
AMP PEAK 2(1Q21.3) WILD-TYPE	104	142	33	2

Figure S8. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S9. Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 2(1Q21.3) MUTATED	23	42	5	61	12
AMP PEAK 2(1Q21.3) WILD-TYPE	22	68	46	39	75

Figure S9. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.05

Table S10. Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 2(1Q21.3) MUTATED	10	37	35	22	26
AMP PEAK 2(1Q21.3) WILD-TYPE	20	55	47	71	33

Figure S10. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00467 (Fisher's exact test), Q value = 0.0086

Table S11. Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 2(1Q21.3) MUTATED	65	20	27	18
AMP PEAK 2(1Q21.3) WILD-TYPE	75	38	51	62

Figure S11. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S12. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 2(1Q21.3) MUTATED	61	18	28	25	19
AMP PEAK 2(1Q21.3) WILD-TYPE	33	76	65	57	31

Figure S12. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00051

Table S13. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 2(1Q21.3) MUTATED	43	14	61	33
AMP PEAK 2(1Q21.3) WILD-TYPE	66	68	74	54

Figure S13. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S14. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 2(1Q21.3) MUTATED	31	14	28	25	13	46
AMP PEAK 2(1Q21.3) WILD-TYPE	30	52	52	86	37	20

Figure S14. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S15. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 2(1Q21.3) MUTATED	74	19	64
AMP PEAK 2(1Q21.3) WILD-TYPE	169	63	45

Figure S15. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.0058

Table S16. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 2(1Q21.3) MUTATED	66	34	19
AMP PEAK 2(1Q21.3) WILD-TYPE	81	87	54

Figure S16. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S17. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 2(1Q21.3) MUTATED	32	11	10	38	28
AMP PEAK 2(1Q21.3) WILD-TYPE	71	61	34	24	32

Figure S17. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S18. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 3(1Q42.3) MUTATED	116	15	18	1
AMP PEAK 3(1Q42.3) WILD-TYPE	118	138	33	2

Figure S18. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S19. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 3(1Q42.3) MUTATED	20	33	6	61	14
AMP PEAK 3(1Q42.3) WILD-TYPE	25	77	45	39	73

Figure S19. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0045

Table S20. Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 3(1Q42.3) MUTATED	62	15	29	17
AMP PEAK 3(1Q42.3) WILD-TYPE	78	43	49	63

Figure S20. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S21. Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 3(1Q42.3) MUTATED	57	22	27	19	15
AMP PEAK 3(1Q42.3) WILD-TYPE	37	72	66	63	35

Figure S21. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.02

Table S22. Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 3(1Q42.3) MUTATED	32	19	59	30
AMP PEAK 3(1Q42.3) WILD-TYPE	77	63	76	57

Figure S22. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S23. Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 3(1Q42.3) MUTATED	25	9	28	30	10	46
AMP PEAK 3(1Q42.3) WILD-TYPE	36	57	52	81	40	20

Figure S23. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S24. Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 3(1Q42.3) MUTATED	62	22	64
AMP PEAK 3(1Q42.3) WILD-TYPE	181	60	45

Figure S24. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S25. Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 3(1Q42.3) MUTATED	28	18	10	38	20
AMP PEAK 3(1Q42.3) WILD-TYPE	75	54	34	24	40

Figure S25. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S26. Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 4(3Q26.2) MUTATED	121	25	16	2
AMP PEAK 4(3Q26.2) WILD-TYPE	113	128	35	1

Figure S26. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S27. Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 4(3Q26.2) MUTATED	23	33	21	52	17
AMP PEAK 4(3Q26.2) WILD-TYPE	22	77	30	48	70

Figure S27. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.035

Table S28. Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 4(3Q26.2) MUTATED	44	27	34	37	13
AMP PEAK 4(3Q26.2) WILD-TYPE	50	67	59	45	37

Figure S28. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S29. Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 4(3Q26.2) MUTATED	54	20	62	19
AMP PEAK 4(3Q26.2) WILD-TYPE	55	62	73	68

Figure S29. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00561 (Fisher's exact test), Q value = 0.01

Table S30. Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 4(3Q26.2) MUTATED	85	23	54
AMP PEAK 4(3Q26.2) WILD-TYPE	158	59	55

Figure S30. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00081

Table S31. Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 4(3Q26.2) MUTATED	36	16	11	36	24
AMP PEAK 4(3Q26.2) WILD-TYPE	67	56	33	26	36

Figure S31. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S32. Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 5(5P15.33) MUTATED	100	11	17	2
AMP PEAK 5(5P15.33) WILD-TYPE	134	142	34	1

Figure S32. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S33. Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 5(5P15.33) MUTATED	13	23	8	60	13
AMP PEAK 5(5P15.33) WILD-TYPE	32	87	43	40	74

Figure S33. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.052

Table S34. Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 5(5P15.33) MUTATED	7	28	28	14	17
AMP PEAK 5(5P15.33) WILD-TYPE	23	64	54	79	42

Figure S34. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.055

Table S35. Gene #5: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 5(5P15.33) MUTATED	48	15	17	14
AMP PEAK 5(5P15.33) WILD-TYPE	92	43	61	66

Figure S35. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S36. Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 5(5P15.33) MUTATED	56	12	18	21	17
AMP PEAK 5(5P15.33) WILD-TYPE	38	82	75	61	33

Figure S36. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S37. Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 5(5P15.33) MUTATED	34	10	56	24
AMP PEAK 5(5P15.33) WILD-TYPE	75	72	79	63

Figure S37. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S38. Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 5(5P15.33) MUTATED	21	17	16	19	16	39
AMP PEAK 5(5P15.33) WILD-TYPE	40	49	64	92	34	27

Figure S38. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S39. Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 5(5P15.33) MUTATED	58	14	56
AMP PEAK 5(5P15.33) WILD-TYPE	185	68	53

Figure S39. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.0046

Table S40. Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 5(5P15.33) MUTATED	56	23	23
AMP PEAK 5(5P15.33) WILD-TYPE	91	98	50

Figure S40. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S41. Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 5(5P15.33) MUTATED	29	9	12	33	19
AMP PEAK 5(5P15.33) WILD-TYPE	74	63	32	29	41

Figure S41. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S42. Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 6(5P13.1) MUTATED	94	12	18	2
AMP PEAK 6(5P13.1) WILD-TYPE	140	141	33	1

Figure S42. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S43. Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 6(5P13.1) MUTATED	11	25	8	53	14
AMP PEAK 6(5P13.1) WILD-TYPE	34	85	43	47	73

Figure S43. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S44. Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 6(5P13.1) MUTATED	53	16	19	17	14
AMP PEAK 6(5P13.1) WILD-TYPE	41	78	74	65	36

Figure S44. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00051

Table S45. Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 6(5P13.1) MUTATED	29	13	57	20
AMP PEAK 6(5P13.1) WILD-TYPE	80	69	78	67

Figure S45. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S46. Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 6(5P13.1) MUTATED	19	16	17	24	13	36
AMP PEAK 6(5P13.1) WILD-TYPE	42	50	63	87	37	30

Figure S46. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S47. Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 6(5P13.1) MUTATED	53	17	55
AMP PEAK 6(5P13.1) WILD-TYPE	190	65	54

Figure S47. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S48. Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 6(5P13.1) MUTATED	32	12	9	32	14
AMP PEAK 6(5P13.1) WILD-TYPE	71	60	35	30	46

Figure S48. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S49. Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 7(6P21.1) MUTATED	111	5	6	2
AMP PEAK 7(6P21.1) WILD-TYPE	123	148	45	1

Figure S49. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S50. Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 7(6P21.1) MUTATED	13	28	2	59	6
AMP PEAK 7(6P21.1) WILD-TYPE	32	82	49	41	81

Figure S50. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.05

Table S51. Gene #7: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 7(6P21.1) MUTATED	10	36	25	17	16
AMP PEAK 7(6P21.1) WILD-TYPE	20	56	57	76	43

Figure S51. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S52. Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 7(6P21.1) MUTATED	47	14	19	19	19
AMP PEAK 7(6P21.1) WILD-TYPE	47	80	74	63	31

Figure S52. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0028

Table S53. Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 7(6P21.1) MUTATED	33	10	47	28
AMP PEAK 7(6P21.1) WILD-TYPE	76	72	88	59

Figure S53. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S54. Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 7(6P21.1) MUTATED	24	15	19	13	13	38
AMP PEAK 7(6P21.1) WILD-TYPE	37	51	61	98	37	28

Figure S54. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S55. Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 7(6P21.1) MUTATED	58	11	53
AMP PEAK 7(6P21.1) WILD-TYPE	185	71	56

Figure S55. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0035 (Fisher's exact test), Q value = 0.0066

Table S56. Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 7(6P21.1) MUTATED	56	25	17
AMP PEAK 7(6P21.1) WILD-TYPE	91	96	56

Figure S56. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S57. Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 7(6P21.1) MUTATED	25	8	11	34	20
AMP PEAK 7(6P21.1) WILD-TYPE	78	64	33	28	40

Figure S57. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S58. Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 8(6Q12) MUTATED	78	6	4	0
AMP PEAK 8(6Q12) WILD-TYPE	156	147	47	3

Figure S58. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S59. Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 8(6Q12) MUTATED	8	17	1	44	4
AMP PEAK 8(6Q12) WILD-TYPE	37	93	50	56	83

Figure S59. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S60. Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 8(6Q12) MUTATED	40	9	11	12	13
AMP PEAK 8(6Q12) WILD-TYPE	54	85	82	70	37

Figure S60. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00558 (Fisher's exact test), Q value = 0.01

Table S61. Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 8(6Q12) MUTATED	19	8	39	19
AMP PEAK 8(6Q12) WILD-TYPE	90	74	96	68

Figure S61. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S62. Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 8(6Q12) MUTATED	16	11	10	13	5	31
AMP PEAK 8(6Q12) WILD-TYPE	45	55	70	98	45	35

Figure S62. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S63. Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 8(6Q12) MUTATED	39	9	38
AMP PEAK 8(6Q12) WILD-TYPE	204	73	71

Figure S63. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S64. Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 8(6Q12) MUTATED	15	7	5	25	13
AMP PEAK 8(6Q12) WILD-TYPE	88	65	39	37	47

Figure S64. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S65. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 9(6Q21) MUTATED	75	4	3	0
AMP PEAK 9(6Q21) WILD-TYPE	159	149	48	3

Figure S65. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S66. Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 9(6Q21) MUTATED	7	17	1	38	6
AMP PEAK 9(6Q21) WILD-TYPE	38	93	50	62	81

Figure S66. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S67. Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 9(6Q21) MUTATED	39	9	12	7	11
AMP PEAK 9(6Q21) WILD-TYPE	55	85	81	75	39

Figure S67. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S68. Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 9(6Q21) MUTATED	12	8	42	16
AMP PEAK 9(6Q21) WILD-TYPE	97	74	93	71

Figure S68. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S69. Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 9(6Q21) MUTATED	13	12	12	12	4	28
AMP PEAK 9(6Q21) WILD-TYPE	48	54	68	99	46	38

Figure S69. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S70. Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 9(6Q21) MUTATED	36	6	39
AMP PEAK 9(6Q21) WILD-TYPE	207	76	70

Figure S70. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S71. Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 9(6Q21) MUTATED	13	5	4	24	15
AMP PEAK 9(6Q21) WILD-TYPE	90	67	40	38	45

Figure S71. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S72. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 10(7P22.1) MUTATED	148	32	47	2
AMP PEAK 10(7P22.1) WILD-TYPE	86	121	4	1

Figure S72. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S73. Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 10(7P22.1) MUTATED	25	62	22	70	25
AMP PEAK 10(7P22.1) WILD-TYPE	20	48	29	30	62

Figure S73. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S74. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 10(7P22.1) MUTATED	67	36	43	35	32
AMP PEAK 10(7P22.1) WILD-TYPE	27	58	50	47	18

Figure S74. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00194 (Fisher's exact test), Q value = 0.0039

Table S75. Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 10(7P22.1) MUTATED	52	29	81	51
AMP PEAK 10(7P22.1) WILD-TYPE	57	53	54	36

Figure S75. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0037

Table S76. Gene #10: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 10(7P22.1) MUTATED	37	31	44	46	20	46
AMP PEAK 10(7P22.1) WILD-TYPE	24	35	36	65	30	20

Figure S76. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00025

Table S77. Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 10(7P22.1) MUTATED	122	29	73
AMP PEAK 10(7P22.1) WILD-TYPE	121	53	36

Figure S77. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00949 (Fisher's exact test), Q value = 0.016

Table S78. Gene #10: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 10(7P22.1) MUTATED	87	49	38
AMP PEAK 10(7P22.1) WILD-TYPE	60	72	35

Figure S78. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0015

Table S79. Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 10(7P22.1) MUTATED	55	22	22	41	34
AMP PEAK 10(7P22.1) WILD-TYPE	48	50	22	21	26

Figure S79. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S80. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 11(7P11.2) MUTATED	131	31	50	2
AMP PEAK 11(7P11.2) WILD-TYPE	103	122	1	1

Figure S80. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 11(7P11.2) MUTATED	21	60	21	65	24
AMP PEAK 11(7P11.2) WILD-TYPE	24	50	30	35	63

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

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0019

Table S82. Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 11(7P11.2) MUTATED	60	34	41	36	30
AMP PEAK 11(7P11.2) WILD-TYPE	34	60	52	46	20

Figure S82. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.067

Table S83. Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 11(7P11.2) MUTATED	53	29	72	47
AMP PEAK 11(7P11.2) WILD-TYPE	56	53	63	40

Figure S83. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.043

Table S84. Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 11(7P11.2) MUTATED	34	29	43	42	21	40
AMP PEAK 11(7P11.2) WILD-TYPE	27	37	37	69	29	26

Figure S84. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0017

Table S85. Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 11(7P11.2) MUTATED	116	27	66
AMP PEAK 11(7P11.2) WILD-TYPE	127	55	43

Figure S85. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.017

Table S86. Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 11(7P11.2) MUTATED	82	45	34
AMP PEAK 11(7P11.2) WILD-TYPE	65	76	39

Figure S86. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00469 (Fisher's exact test), Q value = 0.0086

Table S87. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 11(7P11.2) MUTATED	50	21	20	36	34
AMP PEAK 11(7P11.2) WILD-TYPE	53	51	24	26	26

Figure S87. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S88. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 12(7Q21.2) MUTATED	122	31	50	1
AMP PEAK 12(7Q21.2) WILD-TYPE	112	122	1	2

Figure S88. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S89. Gene #12: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 12(7Q21.2) MUTATED	21	50	21	63	24
AMP PEAK 12(7Q21.2) WILD-TYPE	24	60	30	37	63

Figure S89. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.05

Table S90. Gene #12: 'amp_7q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 12(7Q21.2) MUTATED	49	34	40	38	31
AMP PEAK 12(7Q21.2) WILD-TYPE	45	60	53	44	19

Figure S90. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.032

Table S91. Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 12(7Q21.2) MUTATED	50	27	66	49
AMP PEAK 12(7Q21.2) WILD-TYPE	59	55	69	38

Figure S91. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.06

Table S92. Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 12(7Q21.2) MUTATED	35	32	42	40	18	33
AMP PEAK 12(7Q21.2) WILD-TYPE	26	34	38	71	32	33

Figure S92. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00671 (Fisher's exact test), Q value = 0.012

Table S93. Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 12(7Q21.2) MUTATED	115	26	59
AMP PEAK 12(7Q21.2) WILD-TYPE	128	56	50

Figure S93. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0239 (Fisher's exact test), Q value = 0.037

Table S94. Gene #12: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 12(7Q21.2) MUTATED	75	42	35
AMP PEAK 12(7Q21.2) WILD-TYPE	72	79	38

Figure S94. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.024

Table S95. Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 12(7Q21.2) MUTATED	46	20	22	34	30
AMP PEAK 12(7Q21.2) WILD-TYPE	57	52	22	28	30

Figure S95. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S96. Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 13(7Q22.1) MUTATED	119	31	50	2
AMP PEAK 13(7Q22.1) WILD-TYPE	115	122	1	1

Figure S96. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S97. Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 13(7Q22.1) MUTATED	20	49	21	62	26
AMP PEAK 13(7Q22.1) WILD-TYPE	25	61	30	38	61

Figure S97. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.067

Table S98. Gene #13: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 13(7Q22.1) MUTATED	48	35	39	37	31
AMP PEAK 13(7Q22.1) WILD-TYPE	46	59	54	45	19

Figure S98. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.047

Table S99. Gene #13: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 13(7Q22.1) MUTATED	112	28	58
AMP PEAK 13(7Q22.1) WILD-TYPE	131	54	51

Figure S99. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.06

Table S100. Gene #13: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 13(7Q22.1) MUTATED	76	44	33
AMP PEAK 13(7Q22.1) WILD-TYPE	71	77	40

Figure S100. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.043

Table S101. Gene #13: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 13(7Q22.1) MUTATED	47	21	20	33	32
AMP PEAK 13(7Q22.1) WILD-TYPE	56	51	24	29	28

Figure S101. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0014

Table S102. Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 14(8P23.1) MUTATED	79	78	17	3
AMP PEAK 14(8P23.1) WILD-TYPE	155	75	34	0

Figure S102. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S103. Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 14(8P23.1) MUTATED	12	66	18	31	27
AMP PEAK 14(8P23.1) WILD-TYPE	33	44	33	69	60

Figure S103. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.029

Table S104. Gene #14: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 14(8P23.1) MUTATED	51	37	40	39
AMP PEAK 14(8P23.1) WILD-TYPE	58	45	95	48

Figure S104. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 0.00742 (Fisher's exact test), Q value = 0.013

Table S105. Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 15(8Q24.21) MUTATED	177	92	37	3
AMP PEAK 15(8Q24.21) WILD-TYPE	57	61	14	0

Figure S105. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S106. Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 15(8Q24.21) MUTATED	25	89	23	87	48
AMP PEAK 15(8Q24.21) WILD-TYPE	20	21	28	13	39

Figure S106. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S107. Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 15(8Q24.21) MUTATED	85	55	64	50	36
AMP PEAK 15(8Q24.21) WILD-TYPE	9	39	29	32	14

Figure S107. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S108. Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 15(8Q24.21) MUTATED	51	46	53	60	36	59
AMP PEAK 15(8Q24.21) WILD-TYPE	10	20	27	51	14	7

Figure S108. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00044

Table S109. Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 15(8Q24.21) MUTATED	165	48	92
AMP PEAK 15(8Q24.21) WILD-TYPE	78	34	17

Figure S109. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.016

Table S110. Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 15(8Q24.21) MUTATED	113	72	52
AMP PEAK 15(8Q24.21) WILD-TYPE	34	49	21

Figure S110. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0014

Table S111. Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 15(8Q24.21) MUTATED	74	37	30	53	43
AMP PEAK 15(8Q24.21) WILD-TYPE	29	35	14	9	17

Figure S111. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0245 (Fisher's exact test), Q value = 0.038

Table S112. Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 16(9P24.1) MUTATED	16	6	30	11
AMP PEAK 16(9P24.1) WILD-TYPE	93	76	105	76

Figure S112. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.05

Table S113. Gene #16: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 16(9P24.1) MUTATED	23	9	14
AMP PEAK 16(9P24.1) WILD-TYPE	124	112	59

Figure S113. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p13.2' versus 'CN_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.059

Table S114. Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 17(9P13.2) MUTATED	59	21	11	0
AMP PEAK 17(9P13.2) WILD-TYPE	175	132	40	3

Figure S114. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0442 (Fisher's exact test), Q value = 0.064

Table S115. Gene #17: 'amp_9p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 17(9P13.2) MUTATED	37	8	18	10
AMP PEAK 17(9P13.2) WILD-TYPE	103	50	60	70

Figure S115. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.056

Table S116. Gene #17: 'amp_9p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 17(9P13.2) MUTATED	25	10	19	18	14
AMP PEAK 17(9P13.2) WILD-TYPE	69	84	74	64	36

Figure S116. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.011

Table S117. Gene #17: 'amp_9p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 17(9P13.2) MUTATED	16	13	18	10	12	20
AMP PEAK 17(9P13.2) WILD-TYPE	45	53	62	101	38	46

Figure S117. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S118. Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 18(9Q34.3) MUTATED	78	26	17	1
AMP PEAK 18(9Q34.3) WILD-TYPE	156	127	34	2

Figure S118. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.033

Table S119. Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 18(9Q34.3) MUTATED	16	31	7	36	19
AMP PEAK 18(9Q34.3) WILD-TYPE	29	79	44	64	68

Figure S119. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00743 (Fisher's exact test), Q value = 0.013

Table S120. Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 18(9Q34.3) MUTATED	32	14	29	20	19
AMP PEAK 18(9Q34.3) WILD-TYPE	62	80	64	62	31

Figure S120. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0267 (Fisher's exact test), Q value = 0.041

Table S121. Gene #18: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 18(9Q34.3) MUTATED	24	12	26	22	14	22
AMP PEAK 18(9Q34.3) WILD-TYPE	37	54	54	89	36	44

Figure S121. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S122. Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 19(10P11.22) MUTATED	95	8	16	0
AMP PEAK 19(10P11.22) WILD-TYPE	139	145	35	3

Figure S122. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S123. Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 19(10P11.22) MUTATED	10	29	4	50	14
AMP PEAK 19(10P11.22) WILD-TYPE	35	81	47	50	73

Figure S123. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S124. Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 19(10P11.22) MUTATED	44	16	21	19	14
AMP PEAK 19(10P11.22) WILD-TYPE	50	78	72	63	36

Figure S124. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0038

Table S125. Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 19(10P11.22) MUTATED	22	11	18	22	14	29
AMP PEAK 19(10P11.22) WILD-TYPE	39	55	62	89	36	37

Figure S125. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S126. Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 19(10P11.22) MUTATED	50	17	49
AMP PEAK 19(10P11.22) WILD-TYPE	193	65	60

Figure S126. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.018

Table S127. Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 19(10P11.22) MUTATED	52	26	14
AMP PEAK 19(10P11.22) WILD-TYPE	95	95	59

Figure S127. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S128. Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 19(10P11.22) MUTATED	22	10	8	29	23
AMP PEAK 19(10P11.22) WILD-TYPE	81	62	36	33	37

Figure S128. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S129. Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 20(10Q22.2) MUTATED	71	9	6	0
AMP PEAK 20(10Q22.2) WILD-TYPE	163	144	45	3

Figure S129. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'METHLYATION_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.0041

Table S130. Gene #20: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 20(10Q22.2) MUTATED	15	26	5	23	8
AMP PEAK 20(10Q22.2) WILD-TYPE	30	84	46	77	79

Figure S130. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.019

Table S131. Gene #20: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 20(10Q22.2) MUTATED	27	13	33	8
AMP PEAK 20(10Q22.2) WILD-TYPE	82	69	102	79

Figure S131. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S132. Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 21(10Q26.13) MUTATED	72	11	5	0
AMP PEAK 21(10Q26.13) WILD-TYPE	162	142	46	3

Figure S132. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0021

Table S133. Gene #21: 'amp_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 21(10Q26.13) MUTATED	12	18	4	31	10
AMP PEAK 21(10Q26.13) WILD-TYPE	33	92	47	69	77

Figure S133. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.059

Table S134. Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 21(10Q26.13) MUTATED	29	18	15	13	6
AMP PEAK 21(10Q26.13) WILD-TYPE	65	76	78	69	44

Figure S134. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S135. Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 22(11P13) MUTATED	69	11	8	0
AMP PEAK 22(11P13) WILD-TYPE	165	142	43	3

Figure S135. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.003

Table S136. Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 22(11P13) MUTATED	10	13	8	34	14
AMP PEAK 22(11P13) WILD-TYPE	35	97	43	66	73

Figure S136. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0014

Table S137. Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 22(11P13) MUTATED	14	9	13	17	6	27
AMP PEAK 22(11P13) WILD-TYPE	47	57	67	94	44	39

Figure S137. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S138. Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 22(11P13) MUTATED	35	12	39
AMP PEAK 22(11P13) WILD-TYPE	208	70	70

Figure S138. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0023

Table S139. Gene #22: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 22(11P13) MUTATED	16	10	6	25	10
AMP PEAK 22(11P13) WILD-TYPE	87	62	38	37	50

Figure S139. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S140. Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 23(11P11.2) MUTATED	78	7	7	0
AMP PEAK 23(11P11.2) WILD-TYPE	156	146	44	3

Figure S140. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S141. Gene #23: 'amp_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 23(11P11.2) MUTATED	11	15	8	38	9
AMP PEAK 23(11P11.2) WILD-TYPE	34	95	43	62	78

Figure S141. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0389 (Fisher's exact test), Q value = 0.058

Table S142. Gene #23: 'amp_11p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 23(11P11.2) MUTATED	35	6	20	12
AMP PEAK 23(11P11.2) WILD-TYPE	105	52	58	68

Figure S142. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0025

Table S143. Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 23(11P11.2) MUTATED	35	14	14	14	10
AMP PEAK 23(11P11.2) WILD-TYPE	59	80	79	68	40

Figure S143. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00973 (Fisher's exact test), Q value = 0.017

Table S144. Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 23(11P11.2) MUTATED	22	9	40	16
AMP PEAK 23(11P11.2) WILD-TYPE	87	73	95	71

Figure S144. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S145. Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 23(11P11.2) MUTATED	18	10	13	12	9	27
AMP PEAK 23(11P11.2) WILD-TYPE	43	56	67	99	41	39

Figure S145. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S146. Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 23(11P11.2) MUTATED	41	6	42
AMP PEAK 23(11P11.2) WILD-TYPE	202	76	67

Figure S146. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0043

Table S147. Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 23(11P11.2) MUTATED	42	18	8
AMP PEAK 23(11P11.2) WILD-TYPE	105	103	65

Figure S147. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S148. Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 23(11P11.2) MUTATED	19	4	6	25	14
AMP PEAK 23(11P11.2) WILD-TYPE	84	68	38	37	46

Figure S148. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S149. Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 24(11Q13.3) MUTATED	95	11	7	2
AMP PEAK 24(11Q13.3) WILD-TYPE	139	142	44	1

Figure S149. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0038

Table S150. Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 24(11Q13.3) MUTATED	16	28	7	37	14
AMP PEAK 24(11Q13.3) WILD-TYPE	29	82	44	63	73

Figure S150. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 0.063

Table S151. Gene #24: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 24(11Q13.3) MUTATED	3	32	23	20	12
AMP PEAK 24(11Q13.3) WILD-TYPE	27	60	59	73	47

Figure S151. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.012

Table S152. Gene #24: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 24(11Q13.3) MUTATED	35	13	24	24	13
AMP PEAK 24(11Q13.3) WILD-TYPE	59	81	69	58	37

Figure S152. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.0041

Table S153. Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 24(11Q13.3) MUTATED	35	10	44	20
AMP PEAK 24(11Q13.3) WILD-TYPE	74	72	91	67

Figure S153. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00083

Table S154. Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 24(11Q13.3) MUTATED	21	11	23	16	13	28
AMP PEAK 24(11Q13.3) WILD-TYPE	40	55	57	95	37	38

Figure S154. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00098

Table S155. Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 24(11Q13.3) MUTATED	64	9	39
AMP PEAK 24(11Q13.3) WILD-TYPE	179	73	70

Figure S155. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S156. Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 24(11Q13.3) MUTATED	52	26	11
AMP PEAK 24(11Q13.3) WILD-TYPE	95	95	62

Figure S156. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.0023

Table S157. Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 24(11Q13.3) MUTATED	32	8	7	23	19
AMP PEAK 24(11Q13.3) WILD-TYPE	71	64	37	39	41

Figure S157. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S158. Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 25(12P12.1) MUTATED	86	19	22	1
AMP PEAK 25(12P12.1) WILD-TYPE	148	134	29	2

Figure S158. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.026

Table S159. Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 25(12P12.1) MUTATED	22	34	12	33	18
AMP PEAK 25(12P12.1) WILD-TYPE	23	76	39	67	69

Figure S159. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.04

Table S160. Gene #25: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 25(12P12.1) MUTATED	55	29	17
AMP PEAK 25(12P12.1) WILD-TYPE	92	92	56

Figure S160. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0011

Table S161. Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 26(12Q15) MUTATED	73	21	14	1
AMP PEAK 26(12Q15) WILD-TYPE	161	132	37	2

Figure S161. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.012

Table S162. Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 26(12Q15) MUTATED	18	21	16	29	13
AMP PEAK 26(12Q15) WILD-TYPE	27	89	35	71	74

Figure S162. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.029

Table S163. Gene #26: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 26(12Q15) MUTATED	12	15	23	15	17
AMP PEAK 26(12Q15) WILD-TYPE	18	77	59	78	42

Figure S163. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S164. Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 27(13Q12.3) MUTATED	113	22	34	1
AMP PEAK 27(13Q12.3) WILD-TYPE	121	131	17	2

Figure S164. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S165. Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 27(13Q12.3) MUTATED	16	39	9	62	25
AMP PEAK 27(13Q12.3) WILD-TYPE	29	71	42	38	62

Figure S165. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S166. Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 27(13Q12.3) MUTATED	56	25	33	17	30
AMP PEAK 27(13Q12.3) WILD-TYPE	38	69	60	65	20

Figure S166. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0025

Table S167. Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 27(13Q12.3) MUTATED	36	21	58	46
AMP PEAK 27(13Q12.3) WILD-TYPE	73	61	77	41

Figure S167. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S168. Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 27(13Q12.3) MUTATED	34	22	31	29	8	43
AMP PEAK 27(13Q12.3) WILD-TYPE	27	44	49	82	42	23

Figure S168. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 3e-04

Table S169. Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 27(13Q12.3) MUTATED	80	26	61
AMP PEAK 27(13Q12.3) WILD-TYPE	163	56	48

Figure S169. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S170. Gene #27: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 27(13Q12.3) MUTATED	34	21	17	41	16
AMP PEAK 27(13Q12.3) WILD-TYPE	69	51	27	21	44

Figure S170. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S171. Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 28(13Q22.1) MUTATED	124	26	31	0
AMP PEAK 28(13Q22.1) WILD-TYPE	110	127	20	3

Figure S171. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S172. Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 28(13Q22.1) MUTATED	17	38	10	69	25
AMP PEAK 28(13Q22.1) WILD-TYPE	28	72	41	31	62

Figure S172. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S173. Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 28(13Q22.1) MUTATED	64	22	36	19	28
AMP PEAK 28(13Q22.1) WILD-TYPE	30	72	57	63	22

Figure S173. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S174. Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 28(13Q22.1) MUTATED	36	19	69	45
AMP PEAK 28(13Q22.1) WILD-TYPE	73	63	66	42

Figure S174. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S175. Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 28(13Q22.1) MUTATED	35	23	27	30	13	49
AMP PEAK 28(13Q22.1) WILD-TYPE	26	43	53	81	37	17

Figure S175. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S176. Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 28(13Q22.1) MUTATED	82	26	69
AMP PEAK 28(13Q22.1) WILD-TYPE	161	56	40

Figure S176. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S177. Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 28(13Q22.1) MUTATED	38	20	17	42	21
AMP PEAK 28(13Q22.1) WILD-TYPE	65	52	27	20	39

Figure S177. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.3' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S178. Gene #29: 'amp_14q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 29(14Q21.3) MUTATED	41	5	8	0
AMP PEAK 29(14Q21.3) WILD-TYPE	193	148	43	3

Figure S178. Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q21.3' versus 'METHLYATION_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.0052

Table S179. Gene #29: 'amp_14q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 29(14Q21.3) MUTATED	10	14	0	16	8
AMP PEAK 29(14Q21.3) WILD-TYPE	35	96	51	84	79

Figure S179. Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q21.3' versus 'MRNASEQ_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.044

Table S180. Gene #29: 'amp_14q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 29(14Q21.3) MUTATED	18	6	7	9	9
AMP PEAK 29(14Q21.3) WILD-TYPE	76	88	86	73	41

Figure S180. Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00912 (Fisher's exact test), Q value = 0.016

Table S181. Gene #29: 'amp_14q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 29(14Q21.3) MUTATED	27	9	5
AMP PEAK 29(14Q21.3) WILD-TYPE	120	112	68

Figure S181. Get High-res Image Gene #29: 'amp_14q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S182. Gene #30: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 30(15Q26.1) MUTATED	97	9	7	0
AMP PEAK 30(15Q26.1) WILD-TYPE	137	144	44	3

Figure S182. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S183. Gene #30: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 30(15Q26.1) MUTATED	21	27	2	41	11
AMP PEAK 30(15Q26.1) WILD-TYPE	24	83	49	59	76

Figure S183. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.019

Table S184. Gene #30: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 30(15Q26.1) MUTATED	46	12	22	11
AMP PEAK 30(15Q26.1) WILD-TYPE	94	46	56	69

Figure S184. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S185. Gene #30: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 30(15Q26.1) MUTATED	39	8	24	20	14
AMP PEAK 30(15Q26.1) WILD-TYPE	55	86	69	62	36

Figure S185. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S186. Gene #30: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 30(15Q26.1) MUTATED	25	6	51	23
AMP PEAK 30(15Q26.1) WILD-TYPE	84	76	84	64

Figure S186. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S187. Gene #30: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 30(15Q26.1) MUTATED	19	17	18	13	12	32
AMP PEAK 30(15Q26.1) WILD-TYPE	42	49	62	98	38	34

Figure S187. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S188. Gene #30: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 30(15Q26.1) MUTATED	61	8	42
AMP PEAK 30(15Q26.1) WILD-TYPE	182	74	67

Figure S188. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00032

Table S189. Gene #30: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
AMP PEAK 30(15Q26.1) MUTATED	51	17	25
AMP PEAK 30(15Q26.1) WILD-TYPE	96	104	48

Figure S189. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0018

Table S190. Gene #30: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 30(15Q26.1) MUTATED	29	7	15	24	18
AMP PEAK 30(15Q26.1) WILD-TYPE	74	65	29	38	42

Figure S190. Get High-res Image Gene #30: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S191. Gene #31: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 31(17Q12) MUTATED	121	11	13	2
AMP PEAK 31(17Q12) WILD-TYPE	113	142	38	1

Figure S191. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S192. Gene #31: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 31(17Q12) MUTATED	16	30	16	59	12
AMP PEAK 31(17Q12) WILD-TYPE	29	80	35	41	75

Figure S192. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 0.00726 (Fisher's exact test), Q value = 0.013

Table S193. Gene #31: 'amp_17q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 31(17Q12) MUTATED	16	37	24	22	14
AMP PEAK 31(17Q12) WILD-TYPE	14	55	58	71	45

Figure S193. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S194. Gene #31: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 31(17Q12) MUTATED	55	7	33	18
AMP PEAK 31(17Q12) WILD-TYPE	85	51	45	62

Figure S194. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S195. Gene #31: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 31(17Q12) MUTATED	54	12	27	28	16
AMP PEAK 31(17Q12) WILD-TYPE	40	82	66	54	34

Figure S195. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S196. Gene #31: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 31(17Q12) MUTATED	39	12	61	25
AMP PEAK 31(17Q12) WILD-TYPE	70	70	74	62

Figure S196. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S197. Gene #31: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 31(17Q12) MUTATED	21	17	26	20	20	40
AMP PEAK 31(17Q12) WILD-TYPE	40	49	54	91	30	26

Figure S197. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S198. Gene #31: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 31(17Q12) MUTATED	71	16	57
AMP PEAK 31(17Q12) WILD-TYPE	172	66	52

Figure S198. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00151 (Fisher's exact test), Q value = 0.0031

Table S199. Gene #31: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 31(17Q12) MUTATED	34	13	16	32	18
AMP PEAK 31(17Q12) WILD-TYPE	69	59	28	30	42

Figure S199. Get High-res Image Gene #31: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S200. Gene #32: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 32(18Q11.2) MUTATED	109	16	15	0
AMP PEAK 32(18Q11.2) WILD-TYPE	125	137	36	3

Figure S200. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S201. Gene #32: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 32(18Q11.2) MUTATED	19	32	6	46	20
AMP PEAK 32(18Q11.2) WILD-TYPE	26	78	45	54	67

Figure S201. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S202. Gene #32: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 32(18Q11.2) MUTATED	47	17	22	33	10
AMP PEAK 32(18Q11.2) WILD-TYPE	47	77	71	49	40

Figure S202. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0023

Table S203. Gene #32: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 32(18Q11.2) MUTATED	46	16	48	19
AMP PEAK 32(18Q11.2) WILD-TYPE	63	66	87	68

Figure S203. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.026

Table S204. Gene #32: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 32(18Q11.2) MUTATED	20	17	22	28	18	33
AMP PEAK 32(18Q11.2) WILD-TYPE	41	49	58	83	32	33

Figure S204. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S205. Gene #32: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 32(18Q11.2) MUTATED	66	20	52
AMP PEAK 32(18Q11.2) WILD-TYPE	177	62	57

Figure S205. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.044

Table S206. Gene #32: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 32(18Q11.2) MUTATED	26	16	11	27	23
AMP PEAK 32(18Q11.2) WILD-TYPE	77	56	33	35	37

Figure S206. Get High-res Image Gene #32: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S207. Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 33(19Q12) MUTATED	104	12	14	0
AMP PEAK 33(19Q12) WILD-TYPE	130	141	37	3

Figure S207. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S208. Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 33(19Q12) MUTATED	11	20	9	62	16
AMP PEAK 33(19Q12) WILD-TYPE	34	90	42	38	71

Figure S208. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00068

Table S209. Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 33(19Q12) MUTATED	9	20	37	15	21
AMP PEAK 33(19Q12) WILD-TYPE	21	72	45	78	38

Figure S209. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00034

Table S210. Gene #33: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 33(19Q12) MUTATED	59	11	17	15
AMP PEAK 33(19Q12) WILD-TYPE	81	47	61	65

Figure S210. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S211. Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 33(19Q12) MUTATED	57	15	18	18	13
AMP PEAK 33(19Q12) WILD-TYPE	37	79	75	64	37

Figure S211. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S212. Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 33(19Q12) MUTATED	26	13	60	22
AMP PEAK 33(19Q12) WILD-TYPE	83	69	75	65

Figure S212. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S213. Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 33(19Q12) MUTATED	18	13	18	26	7	47
AMP PEAK 33(19Q12) WILD-TYPE	43	53	62	85	43	19

Figure S213. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S214. Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 33(19Q12) MUTATED	46	15	68
AMP PEAK 33(19Q12) WILD-TYPE	197	67	41

Figure S214. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S215. Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 33(19Q12) MUTATED	20	13	10	43	18
AMP PEAK 33(19Q12) WILD-TYPE	83	59	34	19	42

Figure S215. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S216. Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 34(19Q13.32) MUTATED	79	13	19	0
AMP PEAK 34(19Q13.32) WILD-TYPE	155	140	32	3

Figure S216. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.32' versus 'METHLYATION_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.0044

Table S217. Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 34(19Q13.32) MUTATED	10	22	12	40	14
AMP PEAK 34(19Q13.32) WILD-TYPE	35	88	39	60	73

Figure S217. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.019

Table S218. Gene #34: 'amp_19q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 34(19Q13.32) MUTATED	45	9	17	12
AMP PEAK 34(19Q13.32) WILD-TYPE	95	49	61	68

Figure S218. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00092

Table S219. Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 34(19Q13.32) MUTATED	40	14	21	20	10
AMP PEAK 34(19Q13.32) WILD-TYPE	54	80	72	62	40

Figure S219. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00335 (Fisher's exact test), Q value = 0.0063

Table S220. Gene #34: 'amp_19q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 34(19Q13.32) MUTATED	22	13	49	21
AMP PEAK 34(19Q13.32) WILD-TYPE	87	69	86	66

Figure S220. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S221. Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 34(19Q13.32) MUTATED	13	12	22	19	10	34
AMP PEAK 34(19Q13.32) WILD-TYPE	48	54	58	92	40	32

Figure S221. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0031

Table S222. Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 34(19Q13.32) MUTATED	53	15	42
AMP PEAK 34(19Q13.32) WILD-TYPE	190	67	67

Figure S222. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.00094

Table S223. Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 34(19Q13.32) MUTATED	27	10	7	28	11
AMP PEAK 34(19Q13.32) WILD-TYPE	76	62	37	34	49

Figure S223. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S224. Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 35(20Q13.2) MUTATED	205	46	39	3
AMP PEAK 35(20Q13.2) WILD-TYPE	29	107	12	0

Figure S224. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S225. Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
AMP PEAK 35(20Q13.2) MUTATED	35	56	36	97	37
AMP PEAK 35(20Q13.2) WILD-TYPE	10	54	15	3	50

Figure S225. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.043

Table S226. Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
AMP PEAK 35(20Q13.2) MUTATED	24	64	57	49	41
AMP PEAK 35(20Q13.2) WILD-TYPE	6	28	25	44	18

Figure S226. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S227. Gene #35: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 35(20Q13.2) MUTATED	112	27	54	42
AMP PEAK 35(20Q13.2) WILD-TYPE	28	31	24	38

Figure S227. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S228. Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 35(20Q13.2) MUTATED	92	46	48	56	35
AMP PEAK 35(20Q13.2) WILD-TYPE	2	48	45	26	15

Figure S228. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S229. Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 35(20Q13.2) MUTATED	74	38	115	50
AMP PEAK 35(20Q13.2) WILD-TYPE	35	44	20	37

Figure S229. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S230. Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 35(20Q13.2) MUTATED	36	39	54	62	32	65
AMP PEAK 35(20Q13.2) WILD-TYPE	25	27	26	49	18	1

Figure S230. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S231. Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 35(20Q13.2) MUTATED	144	42	102
AMP PEAK 35(20Q13.2) WILD-TYPE	99	40	7

Figure S231. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S232. Gene #35: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
AMP PEAK 35(20Q13.2) MUTATED	54	38	30	60	39
AMP PEAK 35(20Q13.2) WILD-TYPE	49	34	14	2	21

Figure S232. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.3' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S233. Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
AMP PEAK 36(XQ27.3) MUTATED	51	14	18	0
AMP PEAK 36(XQ27.3) WILD-TYPE	183	139	33	3

Figure S233. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.033

Table S234. Gene #36: 'amp_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
AMP PEAK 36(XQ27.3) MUTATED	15	10	17	14	17
AMP PEAK 36(XQ27.3) WILD-TYPE	79	84	76	68	33

Figure S234. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0081 (Fisher's exact test), Q value = 0.014

Table S235. Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
AMP PEAK 36(XQ27.3) MUTATED	19	9	19	26
AMP PEAK 36(XQ27.3) WILD-TYPE	90	73	116	61

Figure S235. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq27.3' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0015

Table S236. Gene #36: 'amp_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
AMP PEAK 36(XQ27.3) MUTATED	24	13	14	12	6	12
AMP PEAK 36(XQ27.3) WILD-TYPE	37	53	66	99	44	54

Figure S236. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S237. Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 1(1P36.11) MUTATED	123	5	7	0
DEL PEAK 1(1P36.11) WILD-TYPE	111	148	44	3

Figure S237. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S238. Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 1(1P36.11) MUTATED	27	23	5	52	10
DEL PEAK 1(1P36.11) WILD-TYPE	18	87	46	48	77

Figure S238. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0027

Table S239. Gene #37: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
DEL PEAK 1(1P36.11) MUTATED	12	40	22	16	18
DEL PEAK 1(1P36.11) WILD-TYPE	18	52	60	77	41

Figure S239. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S240. Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 1(1P36.11) MUTATED	50	13	34	11
DEL PEAK 1(1P36.11) WILD-TYPE	90	45	44	69

Figure S240. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S241. Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 1(1P36.11) MUTATED	47	12	25	28	16
DEL PEAK 1(1P36.11) WILD-TYPE	47	82	68	54	34

Figure S241. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00058

Table S242. Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 1(1P36.11) MUTATED	38	11	54	25
DEL PEAK 1(1P36.11) WILD-TYPE	71	71	81	62

Figure S242. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S243. Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 1(1P36.11) MUTATED	15	19	25	18	15	40
DEL PEAK 1(1P36.11) WILD-TYPE	46	47	55	93	35	26

Figure S243. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S244. Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 1(1P36.11) MUTATED	63	14	55
DEL PEAK 1(1P36.11) WILD-TYPE	180	68	54

Figure S244. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00569 (Fisher's exact test), Q value = 0.01

Table S245. Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 1(1P36.11) MUTATED	55	24	24
DEL PEAK 1(1P36.11) WILD-TYPE	92	97	49

Figure S245. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S246. Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 1(1P36.11) MUTATED	31	7	12	33	20
DEL PEAK 1(1P36.11) WILD-TYPE	72	65	32	29	40

Figure S246. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S247. Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 2(1P13.2) MUTATED	80	4	9	0
DEL PEAK 2(1P13.2) WILD-TYPE	154	149	42	3

Figure S247. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S248. Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 2(1P13.2) MUTATED	15	20	6	38	5
DEL PEAK 2(1P13.2) WILD-TYPE	30	90	45	62	82

Figure S248. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'RPPA_CNMF'

P value = 0.00265 (Fisher's exact test), Q value = 0.0051

Table S249. Gene #38: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
DEL PEAK 2(1P13.2) MUTATED	6	16	24	10	20
DEL PEAK 2(1P13.2) WILD-TYPE	24	76	58	83	39

Figure S249. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S250. Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 2(1P13.2) MUTATED	36	6	18	13	14
DEL PEAK 2(1P13.2) WILD-TYPE	58	88	75	69	36

Figure S250. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00058

Table S251. Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 2(1P13.2) MUTATED	21	5	40	21
DEL PEAK 2(1P13.2) WILD-TYPE	88	77	95	66

Figure S251. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0044

Table S252. Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 2(1P13.2) MUTATED	11	11	20	14	9	26
DEL PEAK 2(1P13.2) WILD-TYPE	50	55	60	97	41	40

Figure S252. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00244 (Fisher's exact test), Q value = 0.0047

Table S253. Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 2(1P13.2) MUTATED	48	9	34
DEL PEAK 2(1P13.2) WILD-TYPE	195	73	75

Figure S253. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0207 (Fisher's exact test), Q value = 0.033

Table S254. Gene #38: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 2(1P13.2) MUTATED	41	17	14
DEL PEAK 2(1P13.2) WILD-TYPE	106	104	59

Figure S254. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0013

Table S255. Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 2(1P13.2) MUTATED	24	5	9	23	11
DEL PEAK 2(1P13.2) WILD-TYPE	79	67	35	39	49

Figure S255. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.015

Table S256. Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 3(1Q44) MUTATED	21	2	2	0
DEL PEAK 3(1Q44) WILD-TYPE	213	151	49	3

Figure S256. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.0037

Table S257. Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 3(1Q44) MUTATED	5	5	2	12	0
DEL PEAK 3(1Q44) WILD-TYPE	40	105	49	88	87

Figure S257. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S258. Gene #40: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 4(2Q32.1) MUTATED	49	10	5	0
DEL PEAK 4(2Q32.1) WILD-TYPE	185	143	46	3

Figure S258. Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 9e-04

Table S259. Gene #40: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 4(2Q32.1) MUTATED	9	16	1	24	6
DEL PEAK 4(2Q32.1) WILD-TYPE	36	94	50	76	81

Figure S259. Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.034

Table S260. Gene #40: 'del_2q32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 4(2Q32.1) MUTATED	22	12	7	13	4
DEL PEAK 4(2Q32.1) WILD-TYPE	72	82	86	69	46

Figure S260. Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.0088

Table S261. Gene #40: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 4(2Q32.1) MUTATED	7	5	7	18	6	20
DEL PEAK 4(2Q32.1) WILD-TYPE	54	61	73	93	44	46

Figure S261. Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S262. Gene #40: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 4(2Q32.1) MUTATED	24	10	29
DEL PEAK 4(2Q32.1) WILD-TYPE	219	72	80

Figure S262. Get High-res Image Gene #40: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S263. Gene #41: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 5(2Q33.3) MUTATED	43	4	2	0
DEL PEAK 5(2Q33.3) WILD-TYPE	191	149	49	3

Figure S263. Get High-res Image Gene #41: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0044 (Fisher's exact test), Q value = 0.0081

Table S264. Gene #41: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 5(2Q33.3) MUTATED	25	3	20
DEL PEAK 5(2Q33.3) WILD-TYPE	218	79	89

Figure S264. Get High-res Image Gene #41: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S265. Gene #42: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 6(2Q37.2) MUTATED	66	3	3	0
DEL PEAK 6(2Q37.2) WILD-TYPE	168	150	48	3

Figure S265. Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S266. Gene #42: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 6(2Q37.2) MUTATED	12	13	2	32	8
DEL PEAK 6(2Q37.2) WILD-TYPE	33	97	49	68	79

Figure S266. Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.029

Table S267. Gene #42: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 6(2Q37.2) MUTATED	23	10	11	20	6
DEL PEAK 6(2Q37.2) WILD-TYPE	71	84	82	62	44

Figure S267. Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S268. Gene #42: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 6(2Q37.2) MUTATED	7	6	9	13	11	25
DEL PEAK 6(2Q37.2) WILD-TYPE	54	60	71	98	39	41

Figure S268. Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S269. Gene #42: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 6(2Q37.2) MUTATED	32	6	33
DEL PEAK 6(2Q37.2) WILD-TYPE	211	76	76

Figure S269. Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.016

Table S270. Gene #42: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 6(2Q37.2) MUTATED	15	5	9	18	13
DEL PEAK 6(2Q37.2) WILD-TYPE	88	67	35	44	47

Figure S270. Get High-res Image Gene #42: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S271. Gene #43: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 7(3P26.1) MUTATED	114	6	20	3
DEL PEAK 7(3P26.1) WILD-TYPE	120	147	31	0

Figure S271. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S272. Gene #43: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 7(3P26.1) MUTATED	13	30	10	58	18
DEL PEAK 7(3P26.1) WILD-TYPE	32	80	41	42	69

Figure S272. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S273. Gene #43: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 7(3P26.1) MUTATED	53	17	22	21	20
DEL PEAK 7(3P26.1) WILD-TYPE	41	77	71	61	30

Figure S273. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0023

Table S274. Gene #43: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 7(3P26.1) MUTATED	31	14	56	32
DEL PEAK 7(3P26.1) WILD-TYPE	78	68	79	55

Figure S274. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S275. Gene #43: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 7(3P26.1) MUTATED	21	18	24	25	12	40
DEL PEAK 7(3P26.1) WILD-TYPE	40	48	56	86	38	26

Figure S275. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S276. Gene #43: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 7(3P26.1) MUTATED	66	16	58
DEL PEAK 7(3P26.1) WILD-TYPE	177	66	51

Figure S276. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.032

Table S277. Gene #43: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 7(3P26.1) MUTATED	60	31	20
DEL PEAK 7(3P26.1) WILD-TYPE	87	90	53

Figure S277. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S278. Gene #43: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 7(3P26.1) MUTATED	30	13	15	38	15
DEL PEAK 7(3P26.1) WILD-TYPE	73	59	29	24	45

Figure S278. Get High-res Image Gene #43: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S279. Gene #44: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 8(3P21.1) MUTATED	119	9	22	3
DEL PEAK 8(3P21.1) WILD-TYPE	115	144	29	0

Figure S279. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S280. Gene #44: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 8(3P21.1) MUTATED	23	34	11	53	18
DEL PEAK 8(3P21.1) WILD-TYPE	22	76	40	47	69

Figure S280. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.001

Table S281. Gene #44: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 8(3P21.1) MUTATED	48	21	25	27	19
DEL PEAK 8(3P21.1) WILD-TYPE	46	73	68	55	31

Figure S281. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0036

Table S282. Gene #44: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 8(3P21.1) MUTATED	35	15	58	32
DEL PEAK 8(3P21.1) WILD-TYPE	74	67	77	55

Figure S282. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.021

Table S283. Gene #44: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 8(3P21.1) MUTATED	23	19	29	30	14	35
DEL PEAK 8(3P21.1) WILD-TYPE	38	47	51	81	36	31

Figure S283. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S284. Gene #44: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 8(3P21.1) MUTATED	78	17	55
DEL PEAK 8(3P21.1) WILD-TYPE	165	65	54

Figure S284. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.022

Table S285. Gene #44: 'del_3p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 8(3P21.1) MUTATED	64	33	22
DEL PEAK 8(3P21.1) WILD-TYPE	83	88	51

Figure S285. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.0022

Table S286. Gene #44: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 8(3P21.1) MUTATED	34	15	18	34	18
DEL PEAK 8(3P21.1) WILD-TYPE	69	57	26	28	42

Figure S286. Get High-res Image Gene #44: 'del_3p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S287. Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 9(3P14.2) MUTATED	118	16	20	3
DEL PEAK 9(3P14.2) WILD-TYPE	116	137	31	0

Figure S287. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S288. Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 9(3P14.2) MUTATED	18	38	16	58	14
DEL PEAK 9(3P14.2) WILD-TYPE	27	72	35	42	73

Figure S288. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S289. Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 9(3P14.2) MUTATED	52	15	30	28	21
DEL PEAK 9(3P14.2) WILD-TYPE	42	79	63	54	29

Figure S289. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S290. Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 9(3P14.2) MUTATED	34	14	62	36
DEL PEAK 9(3P14.2) WILD-TYPE	75	68	73	51

Figure S290. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00037

Table S291. Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 9(3P14.2) MUTATED	21	23	27	26	17	40
DEL PEAK 9(3P14.2) WILD-TYPE	40	43	53	85	33	26

Figure S291. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S292. Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 9(3P14.2) MUTATED	78	16	60
DEL PEAK 9(3P14.2) WILD-TYPE	165	66	49

Figure S292. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S293. Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 9(3P14.2) MUTATED	66	28	28
DEL PEAK 9(3P14.2) WILD-TYPE	81	93	45

Figure S293. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S294. Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 9(3P14.2) MUTATED	32	11	20	36	23
DEL PEAK 9(3P14.2) WILD-TYPE	71	61	24	26	37

Figure S294. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S295. Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 10(3Q26.31) MUTATED	40	1	8	0
DEL PEAK 10(3Q26.31) WILD-TYPE	194	152	43	3

Figure S295. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S296. Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 10(3Q26.31) MUTATED	2	11	2	28	2
DEL PEAK 10(3Q26.31) WILD-TYPE	43	99	49	72	85

Figure S296. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S297. Gene #46: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 10(3Q26.31) MUTATED	25	4	6	2	11
DEL PEAK 10(3Q26.31) WILD-TYPE	69	90	87	80	39

Figure S297. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S298. Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 10(3Q26.31) MUTATED	2	6	24	16
DEL PEAK 10(3Q26.31) WILD-TYPE	107	76	111	71

Figure S298. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S299. Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 10(3Q26.31) MUTATED	8	1	11	6	3	19
DEL PEAK 10(3Q26.31) WILD-TYPE	53	65	69	105	47	47

Figure S299. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S300. Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 10(3Q26.31) MUTATED	20	4	24
DEL PEAK 10(3Q26.31) WILD-TYPE	223	78	85

Figure S300. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.022

Table S301. Gene #46: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 10(3Q26.31) MUTATED	10	4	5	15	4
DEL PEAK 10(3Q26.31) WILD-TYPE	93	68	39	47	56

Figure S301. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S302. Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 11(4P16.3) MUTATED	143	11	14	1
DEL PEAK 11(4P16.3) WILD-TYPE	91	142	37	2

Figure S302. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S303. Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 11(4P16.3) MUTATED	20	34	9	58	29
DEL PEAK 11(4P16.3) WILD-TYPE	25	76	42	42	58

Figure S303. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S304. Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 11(4P16.3) MUTATED	59	29	30	24	17
DEL PEAK 11(4P16.3) WILD-TYPE	35	65	63	58	33

Figure S304. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.023

Table S305. Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 11(4P16.3) MUTATED	34	28	67	30
DEL PEAK 11(4P16.3) WILD-TYPE	75	54	68	57

Figure S305. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S306. Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 11(4P16.3) MUTATED	26	12	25	45	14	46
DEL PEAK 11(4P16.3) WILD-TYPE	35	54	55	66	36	20

Figure S306. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S307. Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 11(4P16.3) MUTATED	71	27	70
DEL PEAK 11(4P16.3) WILD-TYPE	172	55	39

Figure S307. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0019

Table S308. Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 11(4P16.3) MUTATED	65	54	15
DEL PEAK 11(4P16.3) WILD-TYPE	82	67	58

Figure S308. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S309. Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 11(4P16.3) MUTATED	39	25	7	45	18
DEL PEAK 11(4P16.3) WILD-TYPE	64	47	37	17	42

Figure S309. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S310. Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 12(4Q22.1) MUTATED	166	12	14	1
DEL PEAK 12(4Q22.1) WILD-TYPE	68	141	37	2

Figure S310. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S311. Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 12(4Q22.1) MUTATED	26	48	9	64	25
DEL PEAK 12(4Q22.1) WILD-TYPE	19	62	42	36	62

Figure S311. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0015

Table S312. Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 12(4Q22.1) MUTATED	58	29	37	33	22
DEL PEAK 12(4Q22.1) WILD-TYPE	36	65	56	49	28

Figure S312. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.035

Table S313. Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 12(4Q22.1) MUTATED	46	25	70	38
DEL PEAK 12(4Q22.1) WILD-TYPE	63	57	65	49

Figure S313. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00959 (Fisher's exact test), Q value = 0.017

Table S314. Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 12(4Q22.1) MUTATED	28	22	34	42	21	42
DEL PEAK 12(4Q22.1) WILD-TYPE	33	44	46	69	29	24

Figure S314. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S315. Gene #48: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 12(4Q22.1) MUTATED	94	28	67
DEL PEAK 12(4Q22.1) WILD-TYPE	149	54	42

Figure S315. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00344 (Fisher's exact test), Q value = 0.0065

Table S316. Gene #48: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 12(4Q22.1) MUTATED	39	24	18	40	25
DEL PEAK 12(4Q22.1) WILD-TYPE	64	48	26	22	35

Figure S316. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S317. Gene #49: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 13(4Q35.1) MUTATED	176	12	15	1
DEL PEAK 13(4Q35.1) WILD-TYPE	58	141	36	2

Figure S317. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S318. Gene #49: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 13(4Q35.1) MUTATED	30	45	10	69	30
DEL PEAK 13(4Q35.1) WILD-TYPE	15	65	41	31	57

Figure S318. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.013

Table S319. Gene #49: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 13(4Q35.1) MUTATED	77	18	39	31
DEL PEAK 13(4Q35.1) WILD-TYPE	63	40	39	49

Figure S319. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S320. Gene #49: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 13(4Q35.1) MUTATED	68	29	35	42	19
DEL PEAK 13(4Q35.1) WILD-TYPE	26	65	58	40	31

Figure S320. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00092

Table S321. Gene #49: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 13(4Q35.1) MUTATED	52	27	81	33
DEL PEAK 13(4Q35.1) WILD-TYPE	57	55	54	54

Figure S321. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00032

Table S322. Gene #49: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 13(4Q35.1) MUTATED	29	22	35	42	27	47
DEL PEAK 13(4Q35.1) WILD-TYPE	32	44	45	69	23	19

Figure S322. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S323. Gene #49: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 13(4Q35.1) MUTATED	101	26	75
DEL PEAK 13(4Q35.1) WILD-TYPE	142	56	34

Figure S323. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00668 (Fisher's exact test), Q value = 0.012

Table S324. Gene #49: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 13(4Q35.1) MUTATED	84	51	27
DEL PEAK 13(4Q35.1) WILD-TYPE	63	70	46

Figure S324. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S325. Gene #49: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 13(4Q35.1) MUTATED	49	22	16	48	27
DEL PEAK 13(4Q35.1) WILD-TYPE	54	50	28	14	33

Figure S325. Get High-res Image Gene #49: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S326. Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 14(5Q12.1) MUTATED	150	3	15	2
DEL PEAK 14(5Q12.1) WILD-TYPE	84	150	36	1

Figure S326. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S327. Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 14(5Q12.1) MUTATED	19	38	5	75	19
DEL PEAK 14(5Q12.1) WILD-TYPE	26	72	46	25	68

Figure S327. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00065

Table S328. Gene #50: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 14(5Q12.1) MUTATED	65	14	32	17
DEL PEAK 14(5Q12.1) WILD-TYPE	75	44	46	63

Figure S328. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S329. Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 14(5Q12.1) MUTATED	74	12	25	28	21
DEL PEAK 14(5Q12.1) WILD-TYPE	20	82	68	54	29

Figure S329. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S330. Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 14(5Q12.1) MUTATED	46	7	78	29
DEL PEAK 14(5Q12.1) WILD-TYPE	63	75	57	58

Figure S330. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S331. Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 14(5Q12.1) MUTATED	27	19	26	20	23	52
DEL PEAK 14(5Q12.1) WILD-TYPE	34	47	54	91	27	14

Figure S331. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S332. Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 14(5Q12.1) MUTATED	77	11	79
DEL PEAK 14(5Q12.1) WILD-TYPE	166	71	30

Figure S332. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0016

Table S333. Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 14(5Q12.1) MUTATED	76	35	28
DEL PEAK 14(5Q12.1) WILD-TYPE	71	86	45

Figure S333. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S334. Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 14(5Q12.1) MUTATED	38	9	17	53	22
DEL PEAK 14(5Q12.1) WILD-TYPE	65	63	27	9	38

Figure S334. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S335. Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 15(5Q23.2) MUTATED	140	3	14	1
DEL PEAK 15(5Q23.2) WILD-TYPE	94	150	37	2

Figure S335. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S336. Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 15(5Q23.2) MUTATED	17	34	7	72	15
DEL PEAK 15(5Q23.2) WILD-TYPE	28	76	44	28	72

Figure S336. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0018

Table S337. Gene #51: 'del_5q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 15(5Q23.2) MUTATED	62	12	31	18
DEL PEAK 15(5Q23.2) WILD-TYPE	78	46	47	62

Figure S337. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_5q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S338. Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 15(5Q23.2) MUTATED	71	10	22	28	19
DEL PEAK 15(5Q23.2) WILD-TYPE	23	84	71	54	31

Figure S338. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S339. Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 15(5Q23.2) MUTATED	41	6	75	28
DEL PEAK 15(5Q23.2) WILD-TYPE	68	76	60	59

Figure S339. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S340. Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 15(5Q23.2) MUTATED	26	13	28	17	20	51
DEL PEAK 15(5Q23.2) WILD-TYPE	35	53	52	94	30	15

Figure S340. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S341. Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 15(5Q23.2) MUTATED	75	9	71
DEL PEAK 15(5Q23.2) WILD-TYPE	168	73	38

Figure S341. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S342. Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 15(5Q23.2) MUTATED	78	30	20
DEL PEAK 15(5Q23.2) WILD-TYPE	69	91	53

Figure S342. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S343. Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 15(5Q23.2) MUTATED	40	8	13	46	21
DEL PEAK 15(5Q23.2) WILD-TYPE	63	64	31	16	39

Figure S343. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S344. Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 16(6P25.3) MUTATED	94	11	10	0
DEL PEAK 16(6P25.3) WILD-TYPE	140	142	41	3

Figure S344. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S345. Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 16(6P25.3) MUTATED	18	31	5	41	13
DEL PEAK 16(6P25.3) WILD-TYPE	27	79	46	59	74

Figure S345. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S346. Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 16(6P25.3) MUTATED	37	9	22	30	7
DEL PEAK 16(6P25.3) WILD-TYPE	57	85	71	52	43

Figure S346. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00072

Table S347. Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 16(6P25.3) MUTATED	33	10	47	15
DEL PEAK 16(6P25.3) WILD-TYPE	76	72	88	72

Figure S347. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.001

Table S348. Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 16(6P25.3) MUTATED	13	12	23	18	17	30
DEL PEAK 16(6P25.3) WILD-TYPE	48	54	57	93	33	36

Figure S348. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S349. Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 16(6P25.3) MUTATED	55	11	47
DEL PEAK 16(6P25.3) WILD-TYPE	188	71	62

Figure S349. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00195 (Fisher's exact test), Q value = 0.0039

Table S350. Gene #52: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 16(6P25.3) MUTATED	52	20	21
DEL PEAK 16(6P25.3) WILD-TYPE	95	101	52

Figure S350. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.0069

Table S351. Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 16(6P25.3) MUTATED	25	9	16	24	19
DEL PEAK 16(6P25.3) WILD-TYPE	78	63	28	38	41

Figure S351. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S352. Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 17(6Q14.1) MUTATED	67	8	12	2
DEL PEAK 17(6Q14.1) WILD-TYPE	167	145	39	1

Figure S352. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00034

Table S353. Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 17(6Q14.1) MUTATED	18	19	5	28	9
DEL PEAK 17(6Q14.1) WILD-TYPE	27	91	46	72	78

Figure S353. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S354. Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 17(6Q14.1) MUTATED	25	7	16	30	6
DEL PEAK 17(6Q14.1) WILD-TYPE	69	87	77	52	44

Figure S354. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00042

Table S355. Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 17(6Q14.1) MUTATED	35	6	30	13
DEL PEAK 17(6Q14.1) WILD-TYPE	74	76	105	74

Figure S355. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.012 (Fisher's exact test), Q value = 0.02

Table S356. Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 17(6Q14.1) MUTATED	50	8	29
DEL PEAK 17(6Q14.1) WILD-TYPE	193	74	80

Figure S356. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.02

Table S357. Gene #53: 'del_6q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 17(6Q14.1) MUTATED	38	14	13
DEL PEAK 17(6Q14.1) WILD-TYPE	109	107	60

Figure S357. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S358. Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 18(6Q24.3) MUTATED	61	5	11	1
DEL PEAK 18(6Q24.3) WILD-TYPE	173	148	40	2

Figure S358. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0011

Table S359. Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 18(6Q24.3) MUTATED	14	14	3	27	10
DEL PEAK 18(6Q24.3) WILD-TYPE	31	96	48	73	77

Figure S359. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00056

Table S360. Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 18(6Q24.3) MUTATED	26	6	12	22	7
DEL PEAK 18(6Q24.3) WILD-TYPE	68	88	81	60	43

Figure S360. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S361. Gene #54: 'del_6q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 18(6Q24.3) MUTATED	26	4	31	12
DEL PEAK 18(6Q24.3) WILD-TYPE	83	78	104	75

Figure S361. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.044

Table S362. Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 18(6Q24.3) MUTATED	42	7	25
DEL PEAK 18(6Q24.3) WILD-TYPE	201	75	84

Figure S362. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.02 (Fisher's exact test), Q value = 0.032

Table S363. Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 18(6Q24.3) MUTATED	34	13	10
DEL PEAK 18(6Q24.3) WILD-TYPE	113	108	63

Figure S363. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0377 (Fisher's exact test), Q value = 0.056

Table S364. Gene #54: 'del_6q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 18(6Q24.3) MUTATED	19	5	5	15	13
DEL PEAK 18(6Q24.3) WILD-TYPE	84	67	39	47	47

Figure S364. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S365. Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 19(6Q26) MUTATED	77	7	17	1
DEL PEAK 19(6Q26) WILD-TYPE	157	146	34	2

Figure S365. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00301 (Fisher's exact test), Q value = 0.0057

Table S366. Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 19(6Q26) MUTATED	18	21	7	31	14
DEL PEAK 19(6Q26) WILD-TYPE	27	89	44	69	73

Figure S366. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S367. Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 19(6Q26) MUTATED	30	10	23	28	5
DEL PEAK 19(6Q26) WILD-TYPE	64	84	70	54	45

Figure S367. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S368. Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 19(6Q26) MUTATED	32	8	45	11
DEL PEAK 19(6Q26) WILD-TYPE	77	74	90	76

Figure S368. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.00434 (Fisher's exact test), Q value = 0.008

Table S369. Gene #55: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 19(6Q26) MUTATED	8	13	24	17	14	24
DEL PEAK 19(6Q26) WILD-TYPE	53	53	56	94	36	42

Figure S369. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.0064

Table S370. Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 19(6Q26) MUTATED	57	9	34
DEL PEAK 19(6Q26) WILD-TYPE	186	73	75

Figure S370. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.034

Table S371. Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 19(6Q26) MUTATED	40	17	19
DEL PEAK 19(6Q26) WILD-TYPE	107	104	54

Figure S371. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00724 (Fisher's exact test), Q value = 0.013

Table S372. Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 19(6Q26) MUTATED	24	7	13	21	11
DEL PEAK 19(6Q26) WILD-TYPE	79	65	31	41	49

Figure S372. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S373. Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 20(7Q31.1) MUTATED	62	7	1	1
DEL PEAK 20(7Q31.1) WILD-TYPE	172	146	50	2

Figure S373. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0026

Table S374. Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 20(7Q31.1) MUTATED	11	20	5	23	4
DEL PEAK 20(7Q31.1) WILD-TYPE	34	90	46	77	83

Figure S374. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00997 (Fisher's exact test), Q value = 0.017

Table S375. Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 20(7Q31.1) MUTATED	27	10	13	13	5
DEL PEAK 20(7Q31.1) WILD-TYPE	67	84	80	69	45

Figure S375. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0298 (Fisher's exact test), Q value = 0.045

Table S376. Gene #56: 'del_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 20(7Q31.1) MUTATED	18	9	32	9
DEL PEAK 20(7Q31.1) WILD-TYPE	91	73	103	78

Figure S376. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0039

Table S377. Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 20(7Q31.1) MUTATED	7	5	12	12	11	21
DEL PEAK 20(7Q31.1) WILD-TYPE	54	61	68	99	39	45

Figure S377. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.05

Table S378. Gene #56: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 20(7Q31.1) MUTATED	32	10	26
DEL PEAK 20(7Q31.1) WILD-TYPE	211	72	83

Figure S378. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0243 (Fisher's exact test), Q value = 0.038

Table S379. Gene #56: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 20(7Q31.1) MUTATED	16	6	4	15	15
DEL PEAK 20(7Q31.1) WILD-TYPE	87	66	40	47	45

Figure S379. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S380. Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 21(7Q36.3) MUTATED	92	3	2	1
DEL PEAK 21(7Q36.3) WILD-TYPE	142	150	49	2

Figure S380. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S381. Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 21(7Q36.3) MUTATED	15	25	3	37	9
DEL PEAK 21(7Q36.3) WILD-TYPE	30	85	48	63	78

Figure S381. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S382. Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 21(7Q36.3) MUTATED	39	13	21	18	3
DEL PEAK 21(7Q36.3) WILD-TYPE	55	81	72	64	47

Figure S382. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S383. Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 21(7Q36.3) MUTATED	27	11	47	9
DEL PEAK 21(7Q36.3) WILD-TYPE	82	71	88	78

Figure S383. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S384. Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 21(7Q36.3) MUTATED	13	10	13	13	14	33
DEL PEAK 21(7Q36.3) WILD-TYPE	48	56	67	98	36	33

Figure S384. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S385. Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 21(7Q36.3) MUTATED	44	8	44
DEL PEAK 21(7Q36.3) WILD-TYPE	199	74	65

Figure S385. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S386. Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 21(7Q36.3) MUTATED	21	5	11	28	16
DEL PEAK 21(7Q36.3) WILD-TYPE	82	67	33	34	44

Figure S386. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S387. Gene #58: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 22(8P23.2) MUTATED	96	5	21	0
DEL PEAK 22(8P23.2) WILD-TYPE	138	148	30	3

Figure S387. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S388. Gene #58: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 22(8P23.2) MUTATED	18	23	4	45	20
DEL PEAK 22(8P23.2) WILD-TYPE	27	87	47	55	67

Figure S388. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S389. Gene #58: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 22(8P23.2) MUTATED	46	12	18	22	16
DEL PEAK 22(8P23.2) WILD-TYPE	48	82	75	60	34

Figure S389. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00058

Table S390. Gene #58: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 22(8P23.2) MUTATED	31	9	51	23
DEL PEAK 22(8P23.2) WILD-TYPE	78	73	84	64

Figure S390. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.032

Table S391. Gene #58: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 22(8P23.2) MUTATED	19	14	22	22	14	29
DEL PEAK 22(8P23.2) WILD-TYPE	42	52	58	89	36	37

Figure S391. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 2e-04

Table S392. Gene #58: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 22(8P23.2) MUTATED	59	13	48
DEL PEAK 22(8P23.2) WILD-TYPE	184	69	61

Figure S392. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S393. Gene #58: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 22(8P23.2) MUTATED	34	9	12	29	13
DEL PEAK 22(8P23.2) WILD-TYPE	69	63	32	33	47

Figure S393. Get High-res Image Gene #58: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S394. Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 23(9P23) MUTATED	162	9	22	2
DEL PEAK 23(9P23) WILD-TYPE	72	144	29	1

Figure S394. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S395. Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 23(9P23) MUTATED	28	40	11	69	28
DEL PEAK 23(9P23) WILD-TYPE	17	70	40	31	59

Figure S395. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00049

Table S396. Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 23(9P23) MUTATED	78	13	33	37
DEL PEAK 23(9P23) WILD-TYPE	62	45	45	43

Figure S396. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S397. Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 23(9P23) MUTATED	65	28	29	43	21
DEL PEAK 23(9P23) WILD-TYPE	29	66	64	39	29

Figure S397. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S398. Gene #59: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 23(9P23) MUTATED	53	24	79	30
DEL PEAK 23(9P23) WILD-TYPE	56	58	56	57

Figure S398. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0025

Table S399. Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 23(9P23) MUTATED	25	23	31	44	24	45
DEL PEAK 23(9P23) WILD-TYPE	36	43	49	67	26	21

Figure S399. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S400. Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 23(9P23) MUTATED	97	27	68
DEL PEAK 23(9P23) WILD-TYPE	146	55	41

Figure S400. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0391 (Fisher's exact test), Q value = 0.058

Table S401. Gene #59: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 23(9P23) MUTATED	78	48	28
DEL PEAK 23(9P23) WILD-TYPE	69	73	45

Figure S401. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0025

Table S402. Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 23(9P23) MUTATED	44	22	22	41	25
DEL PEAK 23(9P23) WILD-TYPE	59	50	22	21	35

Figure S402. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S403. Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 24(9P21.3) MUTATED	166	9	16	2
DEL PEAK 24(9P21.3) WILD-TYPE	68	144	35	1

Figure S403. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S404. Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 24(9P21.3) MUTATED	31	42	2	73	27
DEL PEAK 24(9P21.3) WILD-TYPE	14	68	49	27	60

Figure S404. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0022

Table S405. Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 24(9P21.3) MUTATED	76	14	31	36
DEL PEAK 24(9P21.3) WILD-TYPE	64	44	47	44

Figure S405. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S406. Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 24(9P21.3) MUTATED	68	28	27	40	22
DEL PEAK 24(9P21.3) WILD-TYPE	26	66	66	42	28

Figure S406. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S407. Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 24(9P21.3) MUTATED	54	24	78	29
DEL PEAK 24(9P21.3) WILD-TYPE	55	58	57	58

Figure S407. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S408. Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 24(9P21.3) MUTATED	25	21	27	43	26	48
DEL PEAK 24(9P21.3) WILD-TYPE	36	45	53	68	24	18

Figure S408. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S409. Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 24(9P21.3) MUTATED	94	26	70
DEL PEAK 24(9P21.3) WILD-TYPE	149	56	39

Figure S409. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.05

Table S410. Gene #60: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 24(9P21.3) MUTATED	77	52	25
DEL PEAK 24(9P21.3) WILD-TYPE	70	69	48

Figure S410. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00042

Table S411. Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 24(9P21.3) MUTATED	43	23	19	44	25
DEL PEAK 24(9P21.3) WILD-TYPE	60	49	25	18	35

Figure S411. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S412. Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 25(9Q21.11) MUTATED	102	1	9	1
DEL PEAK 25(9Q21.11) WILD-TYPE	132	152	42	2

Figure S412. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S413. Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 25(9Q21.11) MUTATED	16	23	2	44	19
DEL PEAK 25(9Q21.11) WILD-TYPE	29	87	49	56	68

Figure S413. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00609 (Fisher's exact test), Q value = 0.011

Table S414. Gene #61: 'del_9q21.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 25(9Q21.11) MUTATED	46	6	17	19
DEL PEAK 25(9Q21.11) WILD-TYPE	94	52	61	61

Figure S414. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S415. Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 25(9Q21.11) MUTATED	46	18	16	17	9
DEL PEAK 25(9Q21.11) WILD-TYPE	48	76	77	65	41

Figure S415. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0045

Table S416. Gene #61: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 25(9Q21.11) MUTATED	28	15	49	14
DEL PEAK 25(9Q21.11) WILD-TYPE	81	67	86	73

Figure S416. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00047

Table S417. Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 25(9Q21.11) MUTATED	16	10	17	25	10	33
DEL PEAK 25(9Q21.11) WILD-TYPE	45	56	63	86	40	33

Figure S417. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S418. Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 25(9Q21.11) MUTATED	46	15	50
DEL PEAK 25(9Q21.11) WILD-TYPE	197	67	59

Figure S418. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00025

Table S419. Gene #61: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 25(9Q21.11) MUTATED	20	13	10	32	16
DEL PEAK 25(9Q21.11) WILD-TYPE	83	59	34	30	44

Figure S419. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S420. Gene #62: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 26(10P15.3) MUTATED	61	4	11	1
DEL PEAK 26(10P15.3) WILD-TYPE	173	149	40	2

Figure S420. Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00081

Table S421. Gene #62: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 26(10P15.3) MUTATED	14	17	2	26	9
DEL PEAK 26(10P15.3) WILD-TYPE	31	93	49	74	78

Figure S421. Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.019

Table S422. Gene #62: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 26(10P15.3) MUTATED	24	8	14	20	7
DEL PEAK 26(10P15.3) WILD-TYPE	70	86	79	62	43

Figure S422. Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.052

Table S423. Gene #62: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 26(10P15.3) MUTATED	11	8	18	11	10	18
DEL PEAK 26(10P15.3) WILD-TYPE	50	58	62	100	40	48

Figure S423. Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00338 (Fisher's exact test), Q value = 0.0064

Table S424. Gene #62: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 26(10P15.3) MUTATED	42	6	28
DEL PEAK 26(10P15.3) WILD-TYPE	201	76	81

Figure S424. Get High-res Image Gene #62: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S425. Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 27(10Q22.3) MUTATED	61	2	15	1
DEL PEAK 27(10Q22.3) WILD-TYPE	173	151	36	2

Figure S425. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00061

Table S426. Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 27(10Q22.3) MUTATED	7	14	3	33	13
DEL PEAK 27(10Q22.3) WILD-TYPE	38	96	48	67	74

Figure S426. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S427. Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 27(10Q22.3) MUTATED	34	5	13	12	11
DEL PEAK 27(10Q22.3) WILD-TYPE	60	89	80	70	39

Figure S427. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0014

Table S428. Gene #63: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 27(10Q22.3) MUTATED	18	4	33	20
DEL PEAK 27(10Q22.3) WILD-TYPE	91	78	102	67

Figure S428. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.026

Table S429. Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 27(10Q22.3) MUTATED	15	10	15	10	9	19
DEL PEAK 27(10Q22.3) WILD-TYPE	46	56	65	101	41	47

Figure S429. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S430. Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 27(10Q22.3) MUTATED	37	6	35
DEL PEAK 27(10Q22.3) WILD-TYPE	206	76	74

Figure S430. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.02

Table S431. Gene #63: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 27(10Q22.3) MUTATED	13	5	8	17	13
DEL PEAK 27(10Q22.3) WILD-TYPE	90	67	36	45	47

Figure S431. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S432. Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 28(10Q23.31) MUTATED	95	6	14	1
DEL PEAK 28(10Q23.31) WILD-TYPE	139	147	37	2

Figure S432. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S433. Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 28(10Q23.31) MUTATED	13	23	4	48	14
DEL PEAK 28(10Q23.31) WILD-TYPE	32	87	47	52	73

Figure S433. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.05

Table S434. Gene #64: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
DEL PEAK 28(10Q23.31) MUTATED	13	23	25	15	14
DEL PEAK 28(10Q23.31) WILD-TYPE	17	69	57	78	45

Figure S434. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00797 (Fisher's exact test), Q value = 0.014

Table S435. Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 28(10Q23.31) MUTATED	49	9	17	15
DEL PEAK 28(10Q23.31) WILD-TYPE	91	49	61	65

Figure S435. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S436. Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 28(10Q23.31) MUTATED	49	9	15	20	15
DEL PEAK 28(10Q23.31) WILD-TYPE	45	85	78	62	35

Figure S436. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S437. Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 28(10Q23.31) MUTATED	31	6	47	24
DEL PEAK 28(10Q23.31) WILD-TYPE	78	76	88	63

Figure S437. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00076

Table S438. Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 28(10Q23.31) MUTATED	20	17	18	15	14	30
DEL PEAK 28(10Q23.31) WILD-TYPE	41	49	62	96	36	36

Figure S438. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S439. Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 28(10Q23.31) MUTATED	55	10	49
DEL PEAK 28(10Q23.31) WILD-TYPE	188	72	60

Figure S439. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0019

Table S440. Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 28(10Q23.31) MUTATED	23	8	12	26	18
DEL PEAK 28(10Q23.31) WILD-TYPE	80	64	32	36	42

Figure S440. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S441. Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 29(11P15.5) MUTATED	81	10	6	0
DEL PEAK 29(11P15.5) WILD-TYPE	153	143	45	3

Figure S441. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S442. Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 29(11P15.5) MUTATED	18	20	3	33	9
DEL PEAK 29(11P15.5) WILD-TYPE	27	90	48	67	78

Figure S442. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00212 (Fisher's exact test), Q value = 0.0042

Table S443. Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 29(11P15.5) MUTATED	46	11	10	13
DEL PEAK 29(11P15.5) WILD-TYPE	94	47	68	67

Figure S443. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S444. Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 29(11P15.5) MUTATED	40	10	14	15	8
DEL PEAK 29(11P15.5) WILD-TYPE	54	84	79	67	42

Figure S444. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S445. Gene #65: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 29(11P15.5) MUTATED	23	9	45	10
DEL PEAK 29(11P15.5) WILD-TYPE	86	73	90	77

Figure S445. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.0019

Table S446. Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 29(11P15.5) MUTATED	47	10	37
DEL PEAK 29(11P15.5) WILD-TYPE	196	72	72

Figure S446. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.061

Table S447. Gene #65: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 29(11P15.5) MUTATED	36	16	18
DEL PEAK 29(11P15.5) WILD-TYPE	111	105	55

Figure S447. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.027

Table S448. Gene #65: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 29(11P15.5) MUTATED	16	9	12	21	12
DEL PEAK 29(11P15.5) WILD-TYPE	87	63	32	41	48

Figure S448. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S449. Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 30(11Q23.2) MUTATED	73	10	14	2
DEL PEAK 30(11Q23.2) WILD-TYPE	161	143	37	1

Figure S449. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S450. Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 30(11Q23.2) MUTATED	23	18	5	29	14
DEL PEAK 30(11Q23.2) WILD-TYPE	22	92	46	71	73

Figure S450. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.045

Table S451. Gene #66: 'del_11q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 30(11Q23.2) MUTATED	37	6	19	12
DEL PEAK 30(11Q23.2) WILD-TYPE	103	52	59	68

Figure S451. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 0.00747 (Fisher's exact test), Q value = 0.013

Table S452. Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 30(11Q23.2) MUTATED	30	11	16	22	11
DEL PEAK 30(11Q23.2) WILD-TYPE	64	83	77	60	39

Figure S452. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00837 (Fisher's exact test), Q value = 0.015

Table S453. Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 30(11Q23.2) MUTATED	32	9	34	15
DEL PEAK 30(11Q23.2) WILD-TYPE	77	73	101	72

Figure S453. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.018

Table S454. Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 30(11Q23.2) MUTATED	43	17	16
DEL PEAK 30(11Q23.2) WILD-TYPE	104	104	57

Figure S454. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.033

Table S455. Gene #66: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 30(11Q23.2) MUTATED	22	10	11	23	10
DEL PEAK 30(11Q23.2) WILD-TYPE	81	62	33	39	50

Figure S455. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S456. Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 31(12P13.1) MUTATED	72	3	2	0
DEL PEAK 31(12P13.1) WILD-TYPE	162	150	49	3

Figure S456. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S457. Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 31(12P13.1) MUTATED	11	15	1	38	4
DEL PEAK 31(12P13.1) WILD-TYPE	34	95	50	62	83

Figure S457. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S458. Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 31(12P13.1) MUTATED	35	10	9	12	6
DEL PEAK 31(12P13.1) WILD-TYPE	59	84	84	70	44

Figure S458. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S459. Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 31(12P13.1) MUTATED	16	6	41	9
DEL PEAK 31(12P13.1) WILD-TYPE	93	76	94	78

Figure S459. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0023

Table S460. Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 31(12P13.1) MUTATED	13	9	10	12	8	24
DEL PEAK 31(12P13.1) WILD-TYPE	48	57	70	99	42	42

Figure S460. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0014

Table S461. Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 31(12P13.1) MUTATED	33	10	33
DEL PEAK 31(12P13.1) WILD-TYPE	210	72	76

Figure S461. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00047

Table S462. Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 31(12P13.1) MUTATED	15	5	8	24	13
DEL PEAK 31(12P13.1) WILD-TYPE	88	67	36	38	47

Figure S462. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S463. Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 32(12Q12) MUTATED	52	5	2	0
DEL PEAK 32(12Q12) WILD-TYPE	182	148	49	3

Figure S463. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S464. Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 32(12Q12) MUTATED	14	12	0	23	5
DEL PEAK 32(12Q12) WILD-TYPE	31	98	51	77	82

Figure S464. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MRNASEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.018

Table S465. Gene #68: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 32(12Q12) MUTATED	22	6	9	10	8
DEL PEAK 32(12Q12) WILD-TYPE	72	88	84	72	42

Figure S465. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.031

Table S466. Gene #68: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 32(12Q12) MUTATED	24	10	23
DEL PEAK 32(12Q12) WILD-TYPE	219	72	86

Figure S466. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S467. Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 33(13Q12.11) MUTATED	53	4	5	1
DEL PEAK 33(13Q12.11) WILD-TYPE	181	149	46	2

Figure S467. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.062

Table S468. Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 33(13Q12.11) MUTATED	10	15	3	20	8
DEL PEAK 33(13Q12.11) WILD-TYPE	35	95	48	80	79

Figure S468. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.032

Table S469. Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 33(13Q12.11) MUTATED	18	7	28	7
DEL PEAK 33(13Q12.11) WILD-TYPE	91	75	107	80

Figure S469. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S470. Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 34(14Q23.3) MUTATED	122	7	6	1
DEL PEAK 34(14Q23.3) WILD-TYPE	112	146	45	2

Figure S470. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S471. Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 34(14Q23.3) MUTATED	20	27	9	56	11
DEL PEAK 34(14Q23.3) WILD-TYPE	25	83	42	44	76

Figure S471. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S472. Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 34(14Q23.3) MUTATED	52	19	21	24	10
DEL PEAK 34(14Q23.3) WILD-TYPE	42	75	72	58	40

Figure S472. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S473. Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 34(14Q23.3) MUTATED	35	15	59	17
DEL PEAK 34(14Q23.3) WILD-TYPE	74	67	76	70

Figure S473. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S474. Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 34(14Q23.3) MUTATED	19	11	24	25	15	38
DEL PEAK 34(14Q23.3) WILD-TYPE	42	55	56	86	35	28

Figure S474. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S475. Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 34(14Q23.3) MUTATED	60	15	57
DEL PEAK 34(14Q23.3) WILD-TYPE	183	67	52

Figure S475. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.007

Table S476. Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 34(14Q23.3) MUTATED	58	31	14
DEL PEAK 34(14Q23.3) WILD-TYPE	89	90	59

Figure S476. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S477. Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 34(14Q23.3) MUTATED	34	12	11	33	13
DEL PEAK 34(14Q23.3) WILD-TYPE	69	60	33	29	47

Figure S477. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S478. Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 35(14Q32.32) MUTATED	117	8	8	0
DEL PEAK 35(14Q32.32) WILD-TYPE	117	145	43	3

Figure S478. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S479. Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 35(14Q32.32) MUTATED	24	26	9	47	13
DEL PEAK 35(14Q32.32) WILD-TYPE	21	84	42	53	74

Figure S479. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.012

Table S480. Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 35(14Q32.32) MUTATED	43	23	26	24	10
DEL PEAK 35(14Q32.32) WILD-TYPE	51	71	67	58	40

Figure S480. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.0011

Table S481. Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 35(14Q32.32) MUTATED	32	16	59	19
DEL PEAK 35(14Q32.32) WILD-TYPE	77	66	76	68

Figure S481. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.022

Table S482. Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 35(14Q32.32) MUTATED	17	13	25	30	13	32
DEL PEAK 35(14Q32.32) WILD-TYPE	44	53	55	81	37	34

Figure S482. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00412 (Fisher's exact test), Q value = 0.0076

Table S483. Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 35(14Q32.32) MUTATED	66	18	46
DEL PEAK 35(14Q32.32) WILD-TYPE	177	64	63

Figure S483. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.062

Table S484. Gene #71: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 35(14Q32.32) MUTATED	53	32	15
DEL PEAK 35(14Q32.32) WILD-TYPE	94	89	58

Figure S484. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q32.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.018

Table S485. Gene #71: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 35(14Q32.32) MUTATED	32	15	11	29	13
DEL PEAK 35(14Q32.32) WILD-TYPE	71	57	33	33	47

Figure S485. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S486. Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 36(15Q11.2) MUTATED	102	4	13	1
DEL PEAK 36(15Q11.2) WILD-TYPE	132	149	38	2

Figure S486. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S487. Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 36(15Q11.2) MUTATED	17	26	5	49	13
DEL PEAK 36(15Q11.2) WILD-TYPE	28	84	46	51	74

Figure S487. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0015

Table S488. Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
DEL PEAK 36(15Q11.2) MUTATED	10	20	31	12	21
DEL PEAK 36(15Q11.2) WILD-TYPE	20	72	51	81	38

Figure S488. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0045

Table S489. Gene #72: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 36(15Q11.2) MUTATED	52	14	15	13
DEL PEAK 36(15Q11.2) WILD-TYPE	88	44	63	67

Figure S489. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S490. Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 36(15Q11.2) MUTATED	44	10	20	23	17
DEL PEAK 36(15Q11.2) WILD-TYPE	50	84	73	59	33

Figure S490. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00012

Table S491. Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 36(15Q11.2) MUTATED	30	7	50	27
DEL PEAK 36(15Q11.2) WILD-TYPE	79	75	85	60

Figure S491. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00092

Table S492. Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 36(15Q11.2) MUTATED	23	11	22	18	15	29
DEL PEAK 36(15Q11.2) WILD-TYPE	38	55	58	93	35	37

Figure S492. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S493. Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 36(15Q11.2) MUTATED	58	11	49
DEL PEAK 36(15Q11.2) WILD-TYPE	185	71	60

Figure S493. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S494. Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 36(15Q11.2) MUTATED	30	7	13	26	18
DEL PEAK 36(15Q11.2) WILD-TYPE	73	65	31	36	42

Figure S494. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S495. Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 37(15Q15.1) MUTATED	109	3	10	0
DEL PEAK 37(15Q15.1) WILD-TYPE	125	150	41	3

Figure S495. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S496. Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 37(15Q15.1) MUTATED	21	24	6	47	11
DEL PEAK 37(15Q15.1) WILD-TYPE	24	86	45	53	76

Figure S496. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 0.0024 (Fisher's exact test), Q value = 0.0046

Table S497. Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
DEL PEAK 37(15Q15.1) MUTATED	9	26	27	11	21
DEL PEAK 37(15Q15.1) WILD-TYPE	21	66	55	82	38

Figure S497. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0222 (Fisher's exact test), Q value = 0.035

Table S498. Gene #73: 'del_15q15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 37(15Q15.1) MUTATED	48	16	17	13
DEL PEAK 37(15Q15.1) WILD-TYPE	92	42	61	67

Figure S498. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S499. Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 37(15Q15.1) MUTATED	48	9	22	24	13
DEL PEAK 37(15Q15.1) WILD-TYPE	46	85	71	58	37

Figure S499. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S500. Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 37(15Q15.1) MUTATED	32	5	54	25
DEL PEAK 37(15Q15.1) WILD-TYPE	77	77	81	62

Figure S500. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00098

Table S501. Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 37(15Q15.1) MUTATED	20	13	23	18	15	31
DEL PEAK 37(15Q15.1) WILD-TYPE	41	53	57	93	35	35

Figure S501. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S502. Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 37(15Q15.1) MUTATED	60	10	50
DEL PEAK 37(15Q15.1) WILD-TYPE	183	72	59

Figure S502. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S503. Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 37(15Q15.1) MUTATED	30	5	13	27	17
DEL PEAK 37(15Q15.1) WILD-TYPE	73	67	31	35	43

Figure S503. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S504. Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 38(16P13.3) MUTATED	91	3	2	2
DEL PEAK 38(16P13.3) WILD-TYPE	143	150	49	1

Figure S504. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S505. Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 38(16P13.3) MUTATED	10	22	1	43	13
DEL PEAK 38(16P13.3) WILD-TYPE	35	88	50	57	74

Figure S505. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S506. Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 38(16P13.3) MUTATED	51	8	12	14	5
DEL PEAK 38(16P13.3) WILD-TYPE	43	86	81	68	45

Figure S506. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S507. Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 38(16P13.3) MUTATED	21	8	53	8
DEL PEAK 38(16P13.3) WILD-TYPE	88	74	82	79

Figure S507. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S508. Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 38(16P13.3) MUTATED	12	6	16	16	12	35
DEL PEAK 38(16P13.3) WILD-TYPE	49	60	64	95	38	31

Figure S508. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S509. Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 38(16P13.3) MUTATED	39	9	49
DEL PEAK 38(16P13.3) WILD-TYPE	204	73	60

Figure S509. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00318 (Fisher's exact test), Q value = 0.006

Table S510. Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 38(16P13.3) MUTATED	46	23	9
DEL PEAK 38(16P13.3) WILD-TYPE	101	98	64

Figure S510. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S511. Gene #74: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 38(16P13.3) MUTATED	19	8	3	31	17
DEL PEAK 38(16P13.3) WILD-TYPE	84	64	41	31	43

Figure S511. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S512. Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 39(16Q23.1) MUTATED	134	27	20	1
DEL PEAK 39(16Q23.1) WILD-TYPE	100	126	31	2

Figure S512. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0026

Table S513. Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 39(16Q23.1) MUTATED	16	50	16	55	24
DEL PEAK 39(16Q23.1) WILD-TYPE	29	60	35	45	63

Figure S513. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00536 (Fisher's exact test), Q value = 0.0098

Table S514. Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 39(16Q23.1) MUTATED	54	30	35	32	18
DEL PEAK 39(16Q23.1) WILD-TYPE	40	64	58	50	32

Figure S514. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00022

Table S515. Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 39(16Q23.1) MUTATED	43	22	76	28
DEL PEAK 39(16Q23.1) WILD-TYPE	66	60	59	59

Figure S515. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.01

Table S516. Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 39(16Q23.1) MUTATED	27	23	31	35	23	40
DEL PEAK 39(16Q23.1) WILD-TYPE	34	43	49	76	27	26

Figure S516. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.0066

Table S517. Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 39(16Q23.1) MUTATED	99	23	57
DEL PEAK 39(16Q23.1) WILD-TYPE	144	59	52

Figure S517. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.043

Table S518. Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 39(16Q23.1) MUTATED	71	42	24
DEL PEAK 39(16Q23.1) WILD-TYPE	76	79	49

Figure S518. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0021

Table S519. Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 39(16Q23.1) MUTATED	45	17	14	36	25
DEL PEAK 39(16Q23.1) WILD-TYPE	58	55	30	26	35

Figure S519. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S520. Gene #76: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 40(17P12) MUTATED	160	5	15	1
DEL PEAK 40(17P12) WILD-TYPE	74	148	36	2

Figure S520. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S521. Gene #76: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 40(17P12) MUTATED	28	42	7	72	16
DEL PEAK 40(17P12) WILD-TYPE	17	68	44	28	71

Figure S521. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.027

Table S522. Gene #76: 'del_17p12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	30	92	82	93	59
DEL PEAK 40(17P12) MUTATED	17	45	29	27	25
DEL PEAK 40(17P12) WILD-TYPE	13	47	53	66	34

Figure S522. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0032

Table S523. Gene #76: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 40(17P12) MUTATED	69	16	36	22
DEL PEAK 40(17P12) WILD-TYPE	71	42	42	58

Figure S523. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S524. Gene #76: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 40(17P12) MUTATED	64	17	30	37	20
DEL PEAK 40(17P12) WILD-TYPE	30	77	63	45	30

Figure S524. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S525. Gene #76: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 40(17P12) MUTATED	52	14	69	33
DEL PEAK 40(17P12) WILD-TYPE	57	68	66	54

Figure S525. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S526. Gene #76: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 40(17P12) MUTATED	25	23	31	28	24	45
DEL PEAK 40(17P12) WILD-TYPE	36	43	49	83	26	21

Figure S526. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S527. Gene #76: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 40(17P12) MUTATED	90	16	70
DEL PEAK 40(17P12) WILD-TYPE	153	66	39

Figure S527. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0036

Table S528. Gene #76: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 40(17P12) MUTATED	75	36	29
DEL PEAK 40(17P12) WILD-TYPE	72	85	44

Figure S528. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S529. Gene #76: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 40(17P12) MUTATED	45	14	18	40	23
DEL PEAK 40(17P12) WILD-TYPE	58	58	26	22	37

Figure S529. Get High-res Image Gene #76: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S530. Gene #77: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 41(17Q24.3) MUTATED	67	2	7	0
DEL PEAK 41(17Q24.3) WILD-TYPE	167	151	44	3

Figure S530. Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S531. Gene #77: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 41(17Q24.3) MUTATED	10	18	0	26	10
DEL PEAK 41(17Q24.3) WILD-TYPE	35	92	51	74	77

Figure S531. Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MRNASEQ_CNMF'

P value = 0.00177 (Fisher's exact test), Q value = 0.0036

Table S532. Gene #77: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 41(17Q24.3) MUTATED	26	12	8	12	14
DEL PEAK 41(17Q24.3) WILD-TYPE	68	82	85	70	36

Figure S532. Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.022

Table S533. Gene #77: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 41(17Q24.3) MUTATED	34	11	29
DEL PEAK 41(17Q24.3) WILD-TYPE	209	71	80

Figure S533. Get High-res Image Gene #77: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S534. Gene #78: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 42(18Q12.2) MUTATED	142	15	24	0
DEL PEAK 42(18Q12.2) WILD-TYPE	92	138	27	3

Figure S534. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S535. Gene #78: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 42(18Q12.2) MUTATED	34	32	22	50	21
DEL PEAK 42(18Q12.2) WILD-TYPE	11	78	29	50	66

Figure S535. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S536. Gene #78: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 42(18Q12.2) MUTATED	57	26	38	35	15
DEL PEAK 42(18Q12.2) WILD-TYPE	37	68	55	47	35

Figure S536. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S537. Gene #78: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 42(18Q12.2) MUTATED	46	23	75	27
DEL PEAK 42(18Q12.2) WILD-TYPE	63	59	60	60

Figure S537. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0029

Table S538. Gene #78: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 42(18Q12.2) MUTATED	28	21	37	38	14	40
DEL PEAK 42(18Q12.2) WILD-TYPE	33	45	43	73	36	26

Figure S538. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 7e-04

Table S539. Gene #78: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 42(18Q12.2) MUTATED	91	25	62
DEL PEAK 42(18Q12.2) WILD-TYPE	152	57	47

Figure S539. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00445 (Fisher's exact test), Q value = 0.0082

Table S540. Gene #78: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 42(18Q12.2) MUTATED	73	39	23
DEL PEAK 42(18Q12.2) WILD-TYPE	74	82	50

Figure S540. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S541. Gene #78: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 42(18Q12.2) MUTATED	40	17	17	41	20
DEL PEAK 42(18Q12.2) WILD-TYPE	63	55	27	21	40

Figure S541. Get High-res Image Gene #78: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S542. Gene #79: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 43(18Q21.2) MUTATED	157	19	28	0
DEL PEAK 43(18Q21.2) WILD-TYPE	77	134	23	3

Figure S542. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S543. Gene #79: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 43(18Q21.2) MUTATED	36	41	23	58	24
DEL PEAK 43(18Q21.2) WILD-TYPE	9	69	28	42	63

Figure S543. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S544. Gene #79: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 43(18Q21.2) MUTATED	64	29	43	39	18
DEL PEAK 43(18Q21.2) WILD-TYPE	30	65	50	43	32

Figure S544. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00034

Table S545. Gene #79: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 43(18Q21.2) MUTATED	51	25	82	35
DEL PEAK 43(18Q21.2) WILD-TYPE	58	57	53	52

Figure S545. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.002 (Fisher's exact test), Q value = 0.004

Table S546. Gene #79: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 43(18Q21.2) MUTATED	35	24	41	44	16	41
DEL PEAK 43(18Q21.2) WILD-TYPE	26	42	39	67	34	25

Figure S546. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.001

Table S547. Gene #79: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 43(18Q21.2) MUTATED	106	28	67
DEL PEAK 43(18Q21.2) WILD-TYPE	137	54	42

Figure S547. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00431 (Fisher's exact test), Q value = 0.008

Table S548. Gene #79: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 43(18Q21.2) MUTATED	81	45	27
DEL PEAK 43(18Q21.2) WILD-TYPE	66	76	46

Figure S548. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S549. Gene #79: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 43(18Q21.2) MUTATED	47	20	20	41	25
DEL PEAK 43(18Q21.2) WILD-TYPE	56	52	24	21	35

Figure S549. Get High-res Image Gene #79: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S550. Gene #80: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 44(19P13.3) MUTATED	146	2	13	1
DEL PEAK 44(19P13.3) WILD-TYPE	88	151	38	2

Figure S550. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S551. Gene #80: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 44(19P13.3) MUTATED	15	31	5	81	14
DEL PEAK 44(19P13.3) WILD-TYPE	30	79	46	19	73

Figure S551. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00017

Table S552. Gene #80: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 44(19P13.3) MUTATED	73	14	26	21
DEL PEAK 44(19P13.3) WILD-TYPE	67	44	52	59

Figure S552. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S553. Gene #80: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 44(19P13.3) MUTATED	77	12	22	28	15
DEL PEAK 44(19P13.3) WILD-TYPE	17	82	71	54	35

Figure S553. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S554. Gene #80: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 44(19P13.3) MUTATED	44	7	82	21
DEL PEAK 44(19P13.3) WILD-TYPE	65	75	53	66

Figure S554. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S555. Gene #80: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 44(19P13.3) MUTATED	22	14	23	22	19	59
DEL PEAK 44(19P13.3) WILD-TYPE	39	52	57	89	31	7

Figure S555. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S556. Gene #80: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 44(19P13.3) MUTATED	66	8	85
DEL PEAK 44(19P13.3) WILD-TYPE	177	74	24

Figure S556. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S557. Gene #80: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 44(19P13.3) MUTATED	71	31	25
DEL PEAK 44(19P13.3) WILD-TYPE	76	90	48

Figure S557. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S558. Gene #80: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 44(19P13.3) MUTATED	28	8	18	50	23
DEL PEAK 44(19P13.3) WILD-TYPE	75	64	26	12	37

Figure S558. Get High-res Image Gene #80: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S559. Gene #81: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 45(19Q13.11) MUTATED	70	3	1	1
DEL PEAK 45(19Q13.11) WILD-TYPE	164	150	50	2

Figure S559. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S560. Gene #81: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 45(19Q13.11) MUTATED	7	16	1	40	4
DEL PEAK 45(19Q13.11) WILD-TYPE	38	94	50	60	83

Figure S560. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S561. Gene #81: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 45(19Q13.11) MUTATED	40	3	11	11	7
DEL PEAK 45(19Q13.11) WILD-TYPE	54	91	82	71	43

Figure S561. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S562. Gene #81: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 45(19Q13.11) MUTATED	20	2	38	12
DEL PEAK 45(19Q13.11) WILD-TYPE	89	80	97	75

Figure S562. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S563. Gene #81: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 45(19Q13.11) MUTATED	9	8	11	6	11	29
DEL PEAK 45(19Q13.11) WILD-TYPE	52	58	69	105	39	37

Figure S563. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S564. Gene #81: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 45(19Q13.11) MUTATED	28	4	42
DEL PEAK 45(19Q13.11) WILD-TYPE	215	78	67

Figure S564. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.031

Table S565. Gene #81: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 45(19Q13.11) MUTATED	35	13	12
DEL PEAK 45(19Q13.11) WILD-TYPE	112	108	61

Figure S565. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 6.6e-05

Table S566. Gene #81: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 45(19Q13.11) MUTATED	12	3	5	24	16
DEL PEAK 45(19Q13.11) WILD-TYPE	91	69	39	38	44

Figure S566. Get High-res Image Gene #81: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00221 (Fisher's exact test), Q value = 0.0043

Table S567. Gene #82: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 46(20P12.1) MUTATED	32	5	2	0
DEL PEAK 46(20P12.1) WILD-TYPE	202	148	49	3

Figure S567. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.00167 (Fisher's exact test), Q value = 0.0034

Table S568. Gene #82: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 46(20P12.1) MUTATED	9	6	1	16	5
DEL PEAK 46(20P12.1) WILD-TYPE	36	104	50	84	82

Figure S568. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.024

Table S569. Gene #82: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 46(20P12.1) MUTATED	11	2	9	13	3
DEL PEAK 46(20P12.1) WILD-TYPE	83	92	84	69	47

Figure S569. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.043

Table S570. Gene #82: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 46(20P12.1) MUTATED	15	2	15	6
DEL PEAK 46(20P12.1) WILD-TYPE	94	80	120	81

Figure S570. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.032

Table S571. Gene #82: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 46(20P12.1) MUTATED	3	2	10	6	8	10
DEL PEAK 46(20P12.1) WILD-TYPE	58	64	70	105	42	56

Figure S571. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.044

Table S572. Gene #82: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 46(20P12.1) MUTATED	20	3	16
DEL PEAK 46(20P12.1) WILD-TYPE	223	79	93

Figure S572. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.033

Table S573. Gene #82: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 46(20P12.1) MUTATED	10	1	4	8	10
DEL PEAK 46(20P12.1) WILD-TYPE	93	71	40	54	50

Figure S573. Get High-res Image Gene #82: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S574. Gene #83: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 47(21Q11.2) MUTATED	142	16	22	2
DEL PEAK 47(21Q11.2) WILD-TYPE	92	137	29	1

Figure S574. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S575. Gene #83: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 47(21Q11.2) MUTATED	23	47	7	61	29
DEL PEAK 47(21Q11.2) WILD-TYPE	22	63	44	39	58

Figure S575. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00027

Table S576. Gene #83: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 47(21Q11.2) MUTATED	58	27	36	33	17
DEL PEAK 47(21Q11.2) WILD-TYPE	36	67	57	49	33

Figure S576. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0027 (Fisher's exact test), Q value = 0.0052

Table S577. Gene #83: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 47(21Q11.2) MUTATED	47	22	70	32
DEL PEAK 47(21Q11.2) WILD-TYPE	62	60	65	55

Figure S577. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0038

Table S578. Gene #83: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 47(21Q11.2) MUTATED	25	20	30	39	23	42
DEL PEAK 47(21Q11.2) WILD-TYPE	36	46	50	72	27	24

Figure S578. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S579. Gene #83: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 47(21Q11.2) MUTATED	91	26	62
DEL PEAK 47(21Q11.2) WILD-TYPE	152	56	47

Figure S579. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0019

Table S580. Gene #83: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 47(21Q11.2) MUTATED	79	44	22
DEL PEAK 47(21Q11.2) WILD-TYPE	68	77	51

Figure S580. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0013

Table S581. Gene #83: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 47(21Q11.2) MUTATED	47	22	14	40	22
DEL PEAK 47(21Q11.2) WILD-TYPE	56	50	30	22	38

Figure S581. Get High-res Image Gene #83: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S582. Gene #84: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 48(21Q22.13) MUTATED	153	17	24	2
DEL PEAK 48(21Q22.13) WILD-TYPE	81	136	27	1

Figure S582. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S583. Gene #84: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 48(21Q22.13) MUTATED	26	52	8	60	31
DEL PEAK 48(21Q22.13) WILD-TYPE	19	58	43	40	56

Figure S583. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.13' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S584. Gene #84: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 48(21Q22.13) MUTATED	59	29	42	38	17
DEL PEAK 48(21Q22.13) WILD-TYPE	35	65	51	44	33

Figure S584. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0018

Table S585. Gene #84: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 48(21Q22.13) MUTATED	53	24	75	33
DEL PEAK 48(21Q22.13) WILD-TYPE	56	58	60	54

Figure S585. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0042

Table S586. Gene #84: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 48(21Q22.13) MUTATED	29	22	33	40	27	42
DEL PEAK 48(21Q22.13) WILD-TYPE	32	44	47	71	23	24

Figure S586. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00015

Table S587. Gene #84: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 48(21Q22.13) MUTATED	100	26	67
DEL PEAK 48(21Q22.13) WILD-TYPE	143	56	42

Figure S587. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.01

Table S588. Gene #84: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	147	121	73
DEL PEAK 48(21Q22.13) MUTATED	82	46	28
DEL PEAK 48(21Q22.13) WILD-TYPE	65	75	45

Figure S588. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0029

Table S589. Gene #84: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 48(21Q22.13) MUTATED	51	23	15	40	27
DEL PEAK 48(21Q22.13) WILD-TYPE	52	49	29	22	33

Figure S589. Get High-res Image Gene #84: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S590. Gene #85: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 49(22Q13.31) MUTATED	143	6	12	0
DEL PEAK 49(22Q13.31) WILD-TYPE	91	147	39	3

Figure S590. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S591. Gene #85: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 49(22Q13.31) MUTATED	22	36	6	59	21
DEL PEAK 49(22Q13.31) WILD-TYPE	23	74	45	41	66

Figure S591. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.018

Table S592. Gene #85: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 49(22Q13.31) MUTATED	62	13	29	22
DEL PEAK 49(22Q13.31) WILD-TYPE	78	45	49	58

Figure S592. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0023

Table S593. Gene #85: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 49(22Q13.31) MUTATED	50	23	30	33	16
DEL PEAK 49(22Q13.31) WILD-TYPE	44	71	63	49	34

Figure S593. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0025

Table S594. Gene #85: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	109	82	135	87
DEL PEAK 49(22Q13.31) MUTATED	48	18	60	26
DEL PEAK 49(22Q13.31) WILD-TYPE	61	64	75	61

Figure S594. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S595. Gene #85: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 49(22Q13.31) MUTATED	20	16	28	30	22	42
DEL PEAK 49(22Q13.31) WILD-TYPE	41	50	52	81	28	24

Figure S595. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S596. Gene #85: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 49(22Q13.31) MUTATED	77	17	64
DEL PEAK 49(22Q13.31) WILD-TYPE	166	65	45

Figure S596. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00032

Table S597. Gene #85: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	103	72	44	62	60
DEL PEAK 49(22Q13.31) MUTATED	37	14	16	37	24
DEL PEAK 49(22Q13.31) WILD-TYPE	66	58	28	25	36

Figure S597. Get High-res Image Gene #85: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S598. Gene #86: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 50(XP22.2) MUTATED	70	8	7	0
DEL PEAK 50(XP22.2) WILD-TYPE	164	145	44	3

Figure S598. Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.5e-05

Table S599. Gene #86: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 50(XP22.2) MUTATED	16	21	3	31	8
DEL PEAK 50(XP22.2) WILD-TYPE	29	89	48	69	79

Figure S599. Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.062

Table S600. Gene #86: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	94	94	93	82	50
DEL PEAK 50(XP22.2) MUTATED	25	13	12	15	14
DEL PEAK 50(XP22.2) WILD-TYPE	69	81	81	67	36

Figure S600. Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.04

Table S601. Gene #86: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	61	66	80	111	50	66
DEL PEAK 50(XP22.2) MUTATED	16	10	8	19	11	20
DEL PEAK 50(XP22.2) WILD-TYPE	45	56	72	92	39	46

Figure S601. Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00147 (Fisher's exact test), Q value = 0.003

Table S602. Gene #86: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 50(XP22.2) MUTATED	40	10	34
DEL PEAK 50(XP22.2) WILD-TYPE	203	72	75

Figure S602. Get High-res Image Gene #86: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S603. Gene #87: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 51(XP21.1) MUTATED	63	4	9	0
DEL PEAK 51(XP21.1) WILD-TYPE	171	149	42	3

Figure S603. Get High-res Image Gene #87: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00529 (Fisher's exact test), Q value = 0.0097

Table S604. Gene #87: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 51(XP21.1) MUTATED	15	19	4	21	9
DEL PEAK 51(XP21.1) WILD-TYPE	30	91	47	79	78

Figure S604. Get High-res Image Gene #87: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S605. Gene #88: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	234	153	51	3
DEL PEAK 52(XQ21.33) MUTATED	48	2	7	0
DEL PEAK 52(XQ21.33) WILD-TYPE	186	151	44	3

Figure S605. Get High-res Image Gene #88: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3.6e-05

Table S606. Gene #88: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	45	110	51	100	87
DEL PEAK 52(XQ21.33) MUTATED	17	10	2	15	5
DEL PEAK 52(XQ21.33) WILD-TYPE	28	100	49	85	82

Figure S606. Get High-res Image Gene #88: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.04

Table S607. Gene #88: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 52(XQ21.33) MUTATED	33	4	19
DEL PEAK 52(XQ21.33) WILD-TYPE	210	78	90

Figure S607. Get High-res Image Gene #88: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/22533932/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/22552605/STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly focal cnvs = 88
Number of molecular subtypes = 10
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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