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 89 focal events and 10 molecular subtypes across 441 patients, 609 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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', 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', 'MIRSEQ_MATURE_CNMF', 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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 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 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_9p13.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q26.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q12 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_19q13.32 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_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq27.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
del_1q44 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q33.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_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', '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', 'MIRSEQ_MATURE_CNMF', 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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', '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', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p12.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', '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', and 'MIRSEQ_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_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', 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', 'MIRSEQ_MATURE_CNMF', 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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_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_17p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 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', 'MIRSEQ_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', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', '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', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 89 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, 609 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 (3.79e-05)	1e-05 (3.79e-05)	0.0337 (0.0521)	0.00458 (0.00849)	1e-05 (3.79e-05)	0.00021 (0.000545)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)
amp 5p15 33	130 (29%)	311	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0355 (0.0543)	0.0373 (0.0566)	1e-05 (3.79e-05)	0.00011 (0.000312)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00071 (0.0016)	1e-05 (3.79e-05)
amp 17q12	147 (33%)	294	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00743 (0.0133)	0.0001 (0.000285)	0.0001 (0.000285)	3e-05 (9.89e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00315 (0.00611)	4e-05 (0.000129)
amp 19q12	130 (29%)	311	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00024 (0.00061)	0.0001 (0.000285)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	2e-05 (7.04e-05)	1e-05 (3.79e-05)
amp 20q13 2	293 (66%)	148	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0283 (0.0447)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00021 (0.000545)	1e-05 (3.79e-05)
del 1p36 11	135 (31%)	306	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00161 (0.0033)	0.0001 (0.000285)	0.0001 (0.000285)	0.00245 (0.00487)	3e-05 (9.89e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)
del 10q23 31	116 (26%)	325	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0321 (0.0499)	0.00807 (0.0143)	3e-05 (9.89e-05)	0.0337 (0.0521)	3e-05 (9.89e-05)	1e-05 (3.79e-05)	0.0039 (0.00734)	0.00139 (0.00291)
del 15q11 2	120 (27%)	321	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00062 (0.00142)	0.00246 (0.00487)	1e-05 (3.79e-05)	0.00045 (0.00108)	0.00046 (0.00109)	1e-05 (3.79e-05)	0.0234 (0.0375)	4e-05 (0.000129)
del 15q15 1	122 (28%)	319	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00257 (0.00505)	0.0217 (0.0348)	1e-05 (3.79e-05)	2e-05 (7.04e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0071 (0.0128)	7e-05 (0.00021)
del 17p12	181 (41%)	260	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0169 (0.0279)	0.00144 (0.003)	1e-05 (3.79e-05)	0.00056 (0.0013)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00621 (0.0113)	1e-05 (3.79e-05)
amp 1q42 3	150 (34%)	291	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.349 (0.403)	0.00261 (0.00512)	1e-05 (3.79e-05)	0.014 (0.0234)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00013 (0.000365)
amp 6p21 1	124 (28%)	317	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0336 (0.0521)	0.0559 (0.0811)	0.00014 (0.000389)	0.0359 (0.0547)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	6e-05 (0.000184)	1e-05 (3.79e-05)
amp 11p11 2	92 (21%)	349	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.72 (0.755)	0.0391 (0.0588)	3e-05 (9.89e-05)	0.0001 (0.000285)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00069 (0.00156)	6e-05 (0.000184)
amp 15q26 1	113 (26%)	328	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.146 (0.189)	0.0111 (0.0188)	5e-05 (0.000157)	0.00108 (0.00232)	0.00018 (0.000485)	3e-05 (9.89e-05)	0.00106 (0.00228)	1e-05 (3.79e-05)
amp 19q13 32	111 (25%)	330	1e-05 (3.79e-05)	0.0101 (0.0174)	0.188 (0.234)	0.0118 (0.0199)	8e-05 (0.000235)	0.00737 (0.0132)	0.00093 (0.00202)	0.00111 (0.00238)	0.0102 (0.0174)	0.00158 (0.00326)
del 5q12 1	170 (39%)	271	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.139 (0.181)	0.00018 (0.000485)	1e-05 (3.79e-05)	2e-05 (7.04e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)
del 5q23 2	158 (36%)	283	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.116 (0.155)	0.00074 (0.00165)	1e-05 (3.79e-05)	2e-05 (7.04e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)
del 8p23 3	126 (29%)	315	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0347 (0.0534)	0.0935 (0.128)	1e-05 (3.79e-05)	0.0214 (0.0345)	2e-05 (7.04e-05)	1e-05 (3.79e-05)	0.0411 (0.0612)	1e-05 (3.79e-05)
del 19p13 3	162 (37%)	279	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0548 (0.0799)	7e-05 (0.00021)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)
amp 5p13 1	126 (29%)	315	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.731 (0.763)	0.15 (0.192)	1e-05 (3.79e-05)	0.00103 (0.00222)	6e-05 (0.000184)	1e-05 (3.79e-05)	0.0457 (0.0672)	5e-05 (0.000157)
amp 6q12	88 (20%)	353	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0755 (0.105)	0.577 (0.625)	3e-05 (9.89e-05)	0.00346 (0.00662)	1e-05 (3.79e-05)	7e-05 (0.00021)	5e-05 (0.000157)	2e-05 (7.04e-05)
amp 6q21	82 (19%)	359	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.464 (0.518)	0.469 (0.522)	0.00019 (0.000505)	0.00139 (0.00291)	2e-05 (7.04e-05)	1e-05 (3.79e-05)	0.00019 (0.000505)	1e-05 (3.79e-05)
amp 11q13 3	115 (26%)	326	1e-05 (3.79e-05)	0.00382 (0.00723)	0.0432 (0.064)	0.065 (0.092)	0.0654 (0.0923)	0.0309 (0.0484)	1e-05 (3.79e-05)	0.00036 (0.00088)	0.00142 (0.00297)	0.00041 (0.000992)
del 1p13 2	94 (21%)	347	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0058 (0.0106)	0.176 (0.222)	0.00075 (0.00167)	0.00964 (0.0167)	0.00073 (0.00164)	0.00268 (0.00524)	0.225 (0.273)	0.00019 (0.000505)
del 3p14 2	158 (36%)	283	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.432 (0.485)	0.0901 (0.124)	6e-05 (0.000184)	0.00365 (0.00693)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0338 (0.0521)	1e-05 (3.79e-05)
del 3q26 31	47 (11%)	394	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.527 (0.579)	0.707 (0.747)	0.00027 (0.000683)	0.00854 (0.015)	1e-05 (3.79e-05)	0.00101 (0.00219)	0.00365 (0.00693)	0.00551 (0.0101)
del 4p16 3	169 (38%)	272	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.493 (0.545)	0.474 (0.526)	8e-05 (0.000235)	0.011 (0.0188)	3e-05 (9.89e-05)	1e-05 (3.79e-05)	0.00057 (0.00132)	1e-05 (3.79e-05)
del 4q34 3	200 (45%)	241	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.985 (0.988)	0.014 (0.0234)	8e-05 (0.000235)	0.12 (0.159)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0202 (0.033)	1e-05 (3.79e-05)
del 7q36 3	98 (22%)	343	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.209 (0.256)	0.0652 (0.0922)	2e-05 (7.04e-05)	0.00166 (0.00339)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00159 (0.00327)	1e-05 (3.79e-05)
del 9p21 3	193 (44%)	248	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.44 (0.493)	0.00102 (0.00221)	1e-05 (3.79e-05)	0.0214 (0.0345)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0835 (0.115)	2e-05 (7.04e-05)
del 14q23 3	136 (31%)	305	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.677 (0.719)	0.353 (0.406)	6e-05 (0.000184)	0.00246 (0.00487)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0283 (0.0447)	0.00023 (0.000588)
del 16p13 3	93 (21%)	348	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.838 (0.86)	0.606 (0.651)	1e-05 (3.79e-05)	0.00017 (0.000464)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	1e-05 (3.79e-05)
del 16q23 1	182 (41%)	259	1e-05 (3.79e-05)	0.00049 (0.00115)	0.907 (0.918)	0.153 (0.196)	0.00433 (0.00808)	0.00353 (0.00674)	4e-05 (0.000129)	0.00334 (0.00645)	0.0186 (0.0307)	0.0003 (0.00075)
del 17p13 3	176 (40%)	265	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.336 (0.389)	0.00135 (0.00284)	0.00015 (0.000413)	0.0282 (0.0447)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.077 (0.107)	1e-05 (3.79e-05)
del 18q12 2	181 (41%)	260	1e-05 (3.79e-05)	2e-05 (7.04e-05)	0.342 (0.395)	0.0971 (0.132)	0.0189 (0.0311)	0.00202 (0.00407)	0.00012 (0.000339)	0.00029 (0.000731)	0.00453 (0.00842)	0.0003 (0.00075)
del 18q21 2	204 (46%)	237	1e-05 (3.79e-05)	3e-05 (9.89e-05)	0.533 (0.583)	0.0644 (0.0912)	0.0008 (0.00176)	0.00049 (0.00115)	0.0002 (0.000527)	0.00045 (0.00108)	0.00681 (0.0123)	0.00125 (0.00264)
del 19q13 11	75 (17%)	366	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.322 (0.374)	0.687 (0.728)	0.0003 (0.00075)	0.00919 (0.016)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00223 (0.00446)	1e-05 (3.79e-05)
del 22q13 31	161 (37%)	280	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.879 (0.893)	0.00925 (0.0161)	0.00058 (0.00134)	0.122 (0.161)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.00023 (0.000588)	7e-05 (0.00021)
amp 1p36 22	66 (15%)	375	1e-05 (3.79e-05)	3e-05 (9.89e-05)	0.245 (0.293)	0.521 (0.574)	0.00059 (0.00136)	0.014 (0.0234)	0.0382 (0.0578)	0.0005 (0.00117)	0.129 (0.169)	0.00817 (0.0144)
amp 7p22 1	229 (52%)	212	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.586 (0.632)	0.219 (0.265)	0.00031 (0.000771)	0.0287 (0.0452)	0.00086 (0.00188)	0.0001 (0.000285)	0.188 (0.234)	0.00062 (0.00142)
amp 8q24 21	309 (70%)	132	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.2 (0.247)	0.637 (0.679)	0.003 (0.00583)	0.714 (0.752)	1e-05 (3.79e-05)	0.00019 (0.000505)	0.00014 (0.000389)	0.00026 (0.000659)
amp 10p11 22	119 (27%)	322	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.924 (0.932)	0.273 (0.324)	0.00256 (0.00504)	0.105 (0.141)	0.00127 (0.00268)	5e-05 (0.000157)	0.00339 (0.00652)	6e-05 (0.000184)
amp 11p13	88 (20%)	353	1e-05 (3.79e-05)	0.00046 (0.00109)	0.805 (0.832)	0.141 (0.183)	0.00082 (0.0018)	1e-05 (3.79e-05)	0.00073 (0.00164)	5e-05 (0.000157)	0.104 (0.141)	0.00295 (0.00575)
amp 13q12 3	170 (39%)	271	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0598 (0.0857)	0.534 (0.584)	0.0079 (0.0141)	0.536 (0.586)	8e-05 (0.000235)	0.00011 (0.000312)	0.00343 (0.00658)	0.00063 (0.00143)
amp 13q22 1	181 (41%)	260	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.303 (0.353)	0.407 (0.46)	6e-05 (0.000184)	0.816 (0.842)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	9e-05 (0.000263)	3e-05 (9.89e-05)
del 3p26 1	143 (32%)	298	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.605 (0.651)	0.0904 (0.124)	0.00807 (0.0143)	0.257 (0.307)	2e-05 (7.04e-05)	1e-05 (3.79e-05)	0.00174 (0.00354)	2e-05 (7.04e-05)
del 6p25 3	115 (26%)	326	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.119 (0.159)	0.195 (0.242)	8e-05 (0.000235)	0.0108 (0.0184)	1e-05 (3.79e-05)	2e-05 (7.04e-05)	0.214 (0.262)	0.00022 (0.000568)
del 6q26	102 (23%)	339	2e-05 (7.04e-05)	0.0349 (0.0536)	0.397 (0.45)	0.296 (0.345)	0.00036 (0.00088)	0.0111 (0.0188)	0.0584 (0.0843)	0.00328 (0.00635)	0.0195 (0.032)	0.00077 (0.00171)
del 9p23	195 (44%)	246	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.728 (0.762)	0.00016 (0.000438)	2e-05 (7.04e-05)	0.0975 (0.132)	3e-05 (9.89e-05)	4e-05 (0.000129)	0.354 (0.407)	0.00034 (0.000838)
del 9q21 11	114 (26%)	327	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.902 (0.914)	0.0154 (0.0255)	0.00982 (0.017)	0.566 (0.614)	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.129 (0.169)	0.00047 (0.00112)
del 10q22 3	79 (18%)	362	1e-05 (3.79e-05)	0.00023 (0.000588)	0.809 (0.836)	0.111 (0.149)	0.00045 (0.00108)	0.14 (0.183)	0.00014 (0.000389)	1e-05 (3.79e-05)	0.0399 (0.0596)	0.00021 (0.000545)
del 11p15 5	97 (22%)	344	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.0664 (0.0935)	0.00209 (0.0042)	0.00776 (0.0138)	0.115 (0.154)	0.00024 (0.00061)	0.00081 (0.00178)	0.206 (0.253)	0.00426 (0.00797)
del 12p13 1	77 (17%)	364	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.77 (0.8)	0.189 (0.235)	7e-05 (0.00021)	0.00641 (0.0116)	0.00154 (0.00318)	0.00049 (0.00115)	0.12 (0.159)	0.00862 (0.0151)
del 14q32 32	133 (30%)	308	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.765 (0.797)	0.636 (0.679)	0.00113 (0.00242)	0.00083 (0.00181)	0.00031 (0.000771)	0.00416 (0.00779)	0.0827 (0.114)	0.0015 (0.00311)
del 21q11 2	183 (41%)	258	1e-05 (3.79e-05)	3e-05 (9.89e-05)	0.577 (0.625)	0.148 (0.19)	0.00077 (0.00171)	0.059 (0.0848)	1e-05 (3.79e-05)	0.00063 (0.00143)	0.00503 (0.00927)	0.00018 (0.000485)
del 21q22 3	193 (44%)	248	1e-05 (3.79e-05)	3e-05 (9.89e-05)	0.195 (0.242)	0.108 (0.145)	0.035 (0.0537)	0.0735 (0.103)	6e-05 (0.000184)	0.00033 (0.000818)	0.00061 (0.0014)	0.00018 (0.000485)
del xq21 33	56 (13%)	385	1e-05 (3.79e-05)	0.00387 (0.0073)	0.728 (0.762)	0.0821 (0.114)	0.0252 (0.0403)	0.292 (0.342)	0.0375 (0.0569)	0.0256 (0.0409)	0.0487 (0.0711)	0.0383 (0.0579)
amp 3q26 2	164 (37%)	277	1e-05 (3.79e-05)	0.00019 (0.000505)	0.0587 (0.0845)	0.0634 (0.0901)	0.437 (0.489)	0.419 (0.473)	0.00515 (0.00947)	0.00552 (0.0101)	0.00242 (0.00482)	0.00149 (0.0031)
amp 7p11 2	214 (49%)	227	1e-05 (3.79e-05)	4e-05 (0.000129)	0.602 (0.649)	0.17 (0.216)	0.0384 (0.0579)	0.282 (0.332)	0.00767 (0.0137)	0.00078 (0.00173)	0.273 (0.324)	0.00122 (0.00259)
amp 9p13 2	91 (21%)	350	0.00035 (0.00086)	0.283 (0.333)	0.469 (0.522)	0.0424 (0.0629)	0.048 (0.0703)	0.0459 (0.0674)	0.0418 (0.062)	0.158 (0.201)	0.00074 (0.00165)	0.139 (0.181)
amp 9q34 3	122 (28%)	319	1e-05 (3.79e-05)	0.0131 (0.022)	0.801 (0.829)	0.289 (0.339)	0.0101 (0.0174)	0.0101 (0.0174)	0.0104 (0.0178)	0.213 (0.261)	0.135 (0.176)	0.0047 (0.0087)
amp 18q11 2	140 (32%)	301	1e-05 (3.79e-05)	5e-05 (0.000157)	0.924 (0.932)	0.0609 (0.087)	0.0159 (0.0263)	0.185 (0.232)	2e-05 (7.04e-05)	0.00034 (0.000838)	0.262 (0.313)	0.00399 (0.00749)
del 2q37 2	72 (16%)	369	1e-05 (3.79e-05)	3e-05 (9.89e-05)	0.18 (0.226)	0.306 (0.357)	0.00384 (0.00726)	0.218 (0.265)	0.00015 (0.000413)	5e-05 (0.000157)	0.157 (0.201)	0.00854 (0.015)
del 4q22 1	193 (44%)	248	1e-05 (3.79e-05)	1e-05 (3.79e-05)	0.956 (0.963)	0.0665 (0.0935)	0.0111 (0.0188)	0.237 (0.285)	0.00121 (0.00257)	8e-05 (0.000235)	0.669 (0.712)	0.0002 (0.000527)
del 6q14 1	89 (20%)	352	1e-05 (3.79e-05)	0.00016 (0.000438)	0.186 (0.232)	0.199 (0.245)	0.00151 (0.00313)	0.0411 (0.0612)	0.087 (0.119)	0.0118 (0.0199)	0.226 (0.273)	0.00807 (0.0143)
del 6q24 3	78 (18%)	363	1e-05 (3.79e-05)	0.00173 (0.00352)	0.565 (0.613)	0.606 (0.651)	0.0266 (0.0424)	0.525 (0.577)	0.219 (0.265)	0.0293 (0.0461)	0.0447 (0.066)	0.00335 (0.00645)
del 11q23 2	99 (22%)	342	1e-05 (3.79e-05)	0.00117 (0.0025)	0.232 (0.279)	0.0289 (0.0456)	0.00229 (0.00457)	0.179 (0.226)	0.229 (0.277)	0.0545 (0.0796)	0.0131 (0.022)	0.00908 (0.0158)
amp 7q21 2	204 (46%)	237	1e-05 (3.79e-05)	0.0001 (0.000285)	0.147 (0.189)	0.118 (0.157)	0.292 (0.342)	0.158 (0.201)	0.0277 (0.044)	0.00684 (0.0123)	0.0603 (0.0863)	0.00889 (0.0155)
amp 10q22 2	88 (20%)	353	1e-05 (3.79e-05)	0.0399 (0.0596)	0.841 (0.862)	0.276 (0.326)	0.0392 (0.0588)	0.0354 (0.0542)	0.506 (0.557)	0.267 (0.317)	0.499 (0.552)	0.0097 (0.0168)
del 7q31 1	71 (16%)	370	1e-05 (3.79e-05)	0.00064 (0.00145)	0.879 (0.893)	0.373 (0.425)	0.0143 (0.0238)	0.263 (0.313)	0.00053 (0.00123)	0.0319 (0.0497)	0.128 (0.168)	0.0708 (0.0994)
del 10p12 31	67 (15%)	374	1e-05 (3.79e-05)	0.00166 (0.00339)	0.969 (0.974)	0.17 (0.215)	0.292 (0.342)	0.403 (0.456)	3e-05 (9.89e-05)	0.00049 (0.00115)	0.352 (0.406)	0.021 (0.034)
del 17q24 3	76 (17%)	365	1e-05 (3.79e-05)	5e-05 (0.000157)	0.864 (0.884)	0.428 (0.482)	0.0204 (0.0332)	0.531 (0.582)	0.00627 (0.0114)	0.0135 (0.0227)	0.12 (0.159)	0.484 (0.537)
del 20p12 1	39 (9%)	402	0.00119 (0.00253)	0.00021 (0.000545)	0.361 (0.414)	0.404 (0.457)	0.0212 (0.0343)	0.359 (0.412)	0.00052 (0.00121)	0.0294 (0.0462)	0.663 (0.705)	0.149 (0.192)
amp 7q22 1	202 (46%)	239	1e-05 (3.79e-05)	0.00079 (0.00174)	0.18 (0.226)	0.276 (0.326)	0.683 (0.725)	0.623 (0.667)	0.081 (0.113)	0.0309 (0.0484)	0.144 (0.187)	0.00564 (0.0103)
amp 10q26 13	88 (20%)	353	1e-05 (3.79e-05)	0.00015 (0.000413)	0.631 (0.675)	0.322 (0.374)	0.0111 (0.0188)	0.0592 (0.0851)	0.505 (0.557)	0.0869 (0.119)	0.876 (0.893)	0.0387 (0.0582)
amp 12p12 1	128 (29%)	313	1e-05 (3.79e-05)	0.031 (0.0484)	0.125 (0.164)	0.288 (0.339)	0.208 (0.256)	0.379 (0.431)	0.00651 (0.0118)	0.255 (0.305)	0.49 (0.543)	0.0399 (0.0596)
amp 12q15	109 (25%)	332	1e-05 (3.79e-05)	0.0193 (0.0317)	0.0175 (0.0289)	0.206 (0.253)	0.258 (0.308)	0.0257 (0.041)	0.0559 (0.0811)	0.0975 (0.132)	0.0632 (0.0899)	0.162 (0.206)
amp xq27 3	86 (20%)	355	3e-05 (9.89e-05)	0.00836 (0.0147)	0.688 (0.728)	0.579 (0.626)	0.38 (0.432)	0.708 (0.747)	0.0445 (0.0658)	0.776 (0.805)	0.105 (0.141)	0.0372 (0.0565)
del 2q32 1	64 (15%)	377	0.00037 (9e-04)	0.00041 (0.000992)	0.833 (0.857)	0.42 (0.473)	0.139 (0.181)	0.559 (0.609)	0.00485 (0.00896)	0.00037 (9e-04)	0.0966 (0.132)	0.0553 (0.0804)
del 13q12 11	63 (14%)	378	1e-05 (3.79e-05)	0.0466 (0.0683)	0.539 (0.588)	0.236 (0.284)	0.195 (0.242)	0.0456 (0.0671)	0.236 (0.284)	0.197 (0.243)	0.977 (0.981)	0.0329 (0.0511)
del xp22 2	85 (19%)	356	1e-05 (3.79e-05)	0.0002 (0.000527)	0.873 (0.891)	0.314 (0.365)	0.00021 (0.000545)	0.33 (0.382)	0.105 (0.141)	0.00176 (0.00357)	0.467 (0.52)	0.24 (0.288)
amp 8p23 1	177 (40%)	264	1e-05 (3.79e-05)	0.00013 (0.000365)	0.153 (0.196)	0.818 (0.842)	0.0576 (0.0832)	0.00278 (0.00543)	0.228 (0.276)	0.163 (0.207)	0.119 (0.159)	0.176 (0.222)
amp 9p24 1	65 (15%)	376	8e-05 (0.000235)	0.0836 (0.115)	0.501 (0.554)	0.727 (0.762)	0.0973 (0.132)	0.00196 (0.00396)	0.0357 (0.0546)	0.364 (0.415)	0.121 (0.16)	0.115 (0.154)
del 1q44	30 (7%)	411	0.00044 (0.00106)	0.00189 (0.00382)	0.461 (0.515)	0.384 (0.436)	0.362 (0.414)	0.0625 (0.0889)	0.0205 (0.0333)	0.163 (0.207)	0.93 (0.938)	0.0826 (0.114)
del 2q33 3	49 (11%)	392	0.00022 (0.000568)	0.0711 (0.0997)	0.0714 (0.0999)	0.43 (0.483)	0.275 (0.325)	0.789 (0.818)	0.0199 (0.0325)	0.00446 (0.0083)	0.204 (0.251)	0.185 (0.232)
del 12q12	59 (13%)	382	1e-05 (3.79e-05)	2e-05 (7.04e-05)	0.761 (0.793)	0.909 (0.919)	0.145 (0.188)	0.372 (0.424)	0.102 (0.138)	0.0189 (0.0311)	0.828 (0.852)	0.0614 (0.0876)
del xp21 1	74 (17%)	367	1e-05 (3.79e-05)	0.00358 (0.00682)	0.987 (0.988)	0.854 (0.874)	0.0204 (0.0332)	0.634 (0.677)	0.218 (0.265)	0.155 (0.198)	0.701 (0.741)	0.881 (0.894)
del 1q44	26 (6%)	415	0.00255 (0.00503)	0.00217 (0.00435)	0.562 (0.611)	0.167 (0.211)	0.732 (0.763)	0.355 (0.407)	0.196 (0.243)	0.96 (0.966)	0.869 (0.888)	0.879 (0.893)
amp 19p13 2	47 (11%)	394	2e-05 (7.04e-05)	0.0574 (0.0831)	0.0841 (0.116)	0.785 (0.814)	0.719 (0.755)	0.715 (0.752)	0.614 (0.659)	1 (1.00)	0.123 (0.162)	0.585 (0.631)

'amp_1p36.22' versus 'CN_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 1(1P36.22) MUTATED	38	6	4	16	2
AMP PEAK 1(1P36.22) WILD-TYPE	85	181	32	60	17

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 = 3e-05 (Fisher's exact test), Q value = 9.9e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 1(1P36.22) MUTATED	31	18	0	9
AMP PEAK 1(1P36.22) WILD-TYPE	93	103	42	97

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 = 0.00059 (Fisher's exact test), Q value = 0.0014

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	62	62	44	40	64
AMP PEAK 1(1P36.22) MUTATED	2	2	6	7	15
AMP PEAK 1(1P36.22) WILD-TYPE	60	60	38	33	49

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 = 0.014 (Fisher's exact test), Q value = 0.023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 1(1P36.22) MUTATED	15	1	16
AMP PEAK 1(1P36.22) WILD-TYPE	95	56	89

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 = 0.0382 (Fisher's exact test), Q value = 0.058

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 1(1P36.22) MUTATED	26	12	27
AMP PEAK 1(1P36.22) WILD-TYPE	146	118	105

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 = 5e-04 (Fisher's exact test), Q value = 0.0012

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 = 0.00817 (Fisher's exact test), Q value = 0.014

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	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 1(1P36.22) MUTATED	18	3	1	12	2	13
AMP PEAK 1(1P36.22) WILD-TYPE	66	54	34	64	26	48

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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 2(1Q21.3) MUTATED	85	16	13	36	10
AMP PEAK 2(1Q21.3) WILD-TYPE	38	171	23	40	9

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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 2(1Q21.3) MUTATED	75	45	4	19
AMP PEAK 2(1Q21.3) WILD-TYPE	49	76	38	87

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 = 0.0337 (Fisher's exact test), Q value = 0.052

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 = 0.00458 (Fisher's exact test), Q value = 0.0085

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 = 3.8e-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	62	62	44	40	64
AMP PEAK 2(1Q21.3) MUTATED	11	9	14	15	49
AMP PEAK 2(1Q21.3) WILD-TYPE	51	53	30	25	15

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 = 0.00021 (Fisher's exact test), Q value = 0.00054

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 2(1Q21.3) MUTATED	52	9	37
AMP PEAK 2(1Q21.3) WILD-TYPE	58	48	68

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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 2(1Q21.3) MUTATED	50	29	78
AMP PEAK 2(1Q21.3) WILD-TYPE	122	101	54

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 2(1Q21.3) MUTATED	46	18	15	16	12	12
AMP PEAK 2(1Q21.3) WILD-TYPE	27	39	44	44	21	47

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 = 3.8e-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	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 2(1Q21.3) MUTATED	39	8	3	27	7	35
AMP PEAK 2(1Q21.3) WILD-TYPE	45	49	32	49	21	26

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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 3(1Q42.3) MUTATED	80	18	11	33	8
AMP PEAK 3(1Q42.3) WILD-TYPE	43	169	25	43	11

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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 3(1Q42.3) MUTATED	70	36	5	23
AMP PEAK 3(1Q42.3) WILD-TYPE	54	85	37	83

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 = 0.00261 (Fisher's exact test), Q value = 0.0051

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 = 3.8e-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	62	62	44	40	64
AMP PEAK 3(1Q42.3) MUTATED	12	12	10	13	44
AMP PEAK 3(1Q42.3) WILD-TYPE	50	50	34	27	20

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 = 0.014 (Fisher's exact test), Q value = 0.023

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 3(1Q42.3) MUTATED	47	12	32
AMP PEAK 3(1Q42.3) WILD-TYPE	63	45	73

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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 3(1Q42.3) MUTATED	37	35	76
AMP PEAK 3(1Q42.3) WILD-TYPE	135	95	56

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 = 3.8e-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_CNMF'

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

Table S25. Gene #3: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 3(1Q42.3) MUTATED	44	10	17	17	13	13
AMP PEAK 3(1Q42.3) WILD-TYPE	29	47	42	43	20	46

Figure S25. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00036

Table S26. Gene #3: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 3(1Q42.3) MUTATED	30	13	5	25	6	35
AMP PEAK 3(1Q42.3) WILD-TYPE	54	44	30	51	22	26

Figure S26. 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 = 3.8e-05

Table S27. Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 4(3Q26.2) MUTATED	64	32	11	44	13
AMP PEAK 4(3Q26.2) WILD-TYPE	59	155	25	32	6

Figure S27. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 5e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 4(3Q26.2) MUTATED	65	36	16	29
AMP PEAK 4(3Q26.2) WILD-TYPE	59	85	26	77

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

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.0095

Table S29. Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 4(3Q26.2) MUTATED	59	39	64
AMP PEAK 4(3Q26.2) WILD-TYPE	113	91	68

Figure S29. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00552 (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_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0048

Table S31. Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 4(3Q26.2) MUTATED	40	21	20	18	12	12
AMP PEAK 4(3Q26.2) WILD-TYPE	33	36	39	42	21	47

Figure S31. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0031

Table S32. Gene #4: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 4(3Q26.2) MUTATED	28	10	13	29	9	34
AMP PEAK 4(3Q26.2) WILD-TYPE	56	47	22	47	19	27

Figure S32. 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 = 3.8e-05

Table S33. Gene #5: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 5(5P15.33) MUTATED	77	18	10	20	5
AMP PEAK 5(5P15.33) WILD-TYPE	46	169	26	56	14

Figure S33. 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 = 3.8e-05

Table S34. Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 5(5P15.33) MUTATED	70	22	7	18
AMP PEAK 5(5P15.33) WILD-TYPE	54	99	35	88

Figure S34. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 0.0355 (Fisher's exact test), Q value = 0.054

Table S35. 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 S35. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.057

Table S36. 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 S36. 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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 5(5P15.33) MUTATED	11	6	9	11	38
AMP PEAK 5(5P15.33) WILD-TYPE	51	56	35	29	26

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

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00031

Table S38. Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 5(5P15.33) MUTATED	45	7	23
AMP PEAK 5(5P15.33) WILD-TYPE	65	50	82

Figure S38. 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 = 3.8e-05

Table S39. Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 5(5P15.33) MUTATED	45	21	62
AMP PEAK 5(5P15.33) WILD-TYPE	127	109	70

Figure S39. 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 = 3.8e-05

Table S40. 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 S40. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0016

Table S41. Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 5(5P15.33) MUTATED	33	15	19	18	11	6
AMP PEAK 5(5P15.33) WILD-TYPE	40	42	40	42	22	53

Figure S41. 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 = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S42. Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 5(5P15.33) MUTATED	29	4	6	26	5	32
AMP PEAK 5(5P15.33) WILD-TYPE	55	53	29	50	23	29

Figure S42. 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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 6(5P13.1) MUTATED	73	17	10	21	5
AMP PEAK 6(5P13.1) WILD-TYPE	50	170	26	55	14

Figure S43. 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 = 3.8e-05

Table S44. Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 6(5P13.1) MUTATED	61	23	7	20
AMP PEAK 6(5P13.1) WILD-TYPE	63	98	35	86

Figure S44. 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 = 3.8e-05

Table S45. Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 6(5P13.1) MUTATED	11	8	9	9	38
AMP PEAK 6(5P13.1) WILD-TYPE	51	54	35	31	26

Figure S45. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0022

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 6(5P13.1) MUTATED	43	8	24
AMP PEAK 6(5P13.1) WILD-TYPE	67	49	81

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

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S47. Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 6(5P13.1) MUTATED	41	26	58
AMP PEAK 6(5P13.1) WILD-TYPE	131	104	74

Figure S47. 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 = 3.8e-05

Table S48. 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 S48. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.067

Table S49. Gene #6: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 6(5P13.1) MUTATED	29	14	16	20	11	9
AMP PEAK 6(5P13.1) WILD-TYPE	44	43	43	40	22	50

Figure S49. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S50. Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 6(5P13.1) MUTATED	22	8	5	29	5	30
AMP PEAK 6(5P13.1) WILD-TYPE	62	49	30	47	23	31

Figure S50. 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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 7(6P21.1) MUTATED	79	8	5	25	7
AMP PEAK 7(6P21.1) WILD-TYPE	44	179	31	51	12

Figure S51. 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 = 3.8e-05

Table S52. Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 7(6P21.1) MUTATED	71	27	1	9
AMP PEAK 7(6P21.1) WILD-TYPE	53	94	41	97

Figure S52. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.052

Table S53. 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 S53. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00039

Table S54. Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 7(6P21.1) MUTATED	10	9	10	11	31
AMP PEAK 7(6P21.1) WILD-TYPE	52	53	34	29	33

Figure S54. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.055

Table S55. Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 7(6P21.1) MUTATED	37	9	25
AMP PEAK 7(6P21.1) WILD-TYPE	73	48	80

Figure S55. 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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 7(6P21.1) MUTATED	43	19	60
AMP PEAK 7(6P21.1) WILD-TYPE	129	111	72

Figure S56. 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 = 3.8e-05

Table S57. 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 S57. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S58. Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 7(6P21.1) MUTATED	37	11	13	19	10	8
AMP PEAK 7(6P21.1) WILD-TYPE	36	46	46	41	23	51

Figure S58. 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 = 1e-05 (Fisher's exact test), Q value = 3.8e-05

Table S59. Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 7(6P21.1) MUTATED	30	4	4	23	5	32
AMP PEAK 7(6P21.1) WILD-TYPE	54	53	31	53	23	29

Figure S59. 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 = 3.8e-05

Table S60. Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 8(6Q12) MUTATED	59	9	4	13	3
AMP PEAK 8(6Q12) WILD-TYPE	64	178	32	63	16

Figure S60. 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 = 3.8e-05

Table S61. Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 8(6Q12) MUTATED	48	18	1	7
AMP PEAK 8(6Q12) WILD-TYPE	76	103	41	99

Figure S61. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S62. Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 8(6Q12) MUTATED	6	6	8	6	28
AMP PEAK 8(6Q12) WILD-TYPE	56	56	36	34	36

Figure S62. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.0066

Table S63. Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 8(6Q12) MUTATED	31	4	19
AMP PEAK 8(6Q12) WILD-TYPE	79	53	86

Figure S63. 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 = 3.8e-05

Table S64. Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 8(6Q12) MUTATED	28	14	44
AMP PEAK 8(6Q12) WILD-TYPE	144	116	88

Figure S64. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S65. 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 S65. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S66. Gene #8: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 8(6Q12) MUTATED	30	7	7	9	7	5
AMP PEAK 8(6Q12) WILD-TYPE	43	50	52	51	26	54

Figure S66. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S67. Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 8(6Q12) MUTATED	17	4	3	13	2	26
AMP PEAK 8(6Q12) WILD-TYPE	67	53	32	63	26	35

Figure S67. 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 = 3.8e-05

Table S68. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 9(6Q21) MUTATED	52	8	4	16	2
AMP PEAK 9(6Q21) WILD-TYPE	71	179	32	60	17

Figure S68. 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 = 3.8e-05

Table S69. Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 9(6Q21) MUTATED	42	18	1	8
AMP PEAK 9(6Q21) WILD-TYPE	82	103	41	98

Figure S69. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 5e-04

Table S70. Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 9(6Q21) MUTATED	7	6	7	5	25
AMP PEAK 9(6Q21) WILD-TYPE	55	56	37	35	39

Figure S70. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0029

Table S71. Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 9(6Q21) MUTATED	30	3	17
AMP PEAK 9(6Q21) WILD-TYPE	80	54	88

Figure S71. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

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

Table S72. Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 9(6Q21) MUTATED	29	10	42
AMP PEAK 9(6Q21) WILD-TYPE	143	120	90

Figure S72. 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 = 3.8e-05

Table S73. 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 S73. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 5e-04

Table S74. Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 9(6Q21) MUTATED	27	7	6	7	8	6
AMP PEAK 9(6Q21) WILD-TYPE	46	50	53	53	25	53

Figure S74. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S75. Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 9(6Q21) MUTATED	17	3	1	15	0	25
AMP PEAK 9(6Q21) WILD-TYPE	67	54	34	61	28	36

Figure S75. 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 = 3.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 10(7P22.1) MUTATED	88	51	34	46	10
AMP PEAK 10(7P22.1) WILD-TYPE	35	136	2	30	9

Figure S76. 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 = 3.8e-05

Table S77. Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 10(7P22.1) MUTATED	83	68	19	34
AMP PEAK 10(7P22.1) WILD-TYPE	41	53	23	72

Figure S77. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00077

Table S78. Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 10(7P22.1) MUTATED	27	25	15	23	46
AMP PEAK 10(7P22.1) WILD-TYPE	35	37	29	17	18

Figure S78. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.045

Table S79. Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 10(7P22.1) MUTATED	64	21	51
AMP PEAK 10(7P22.1) WILD-TYPE	46	36	54

Figure S79. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0019

Table S80. Gene #10: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 10(7P22.1) MUTATED	89	52	83
AMP PEAK 10(7P22.1) WILD-TYPE	83	78	49

Figure S80. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S81. 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 S81. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S82. Gene #10: 'amp_7p22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 10(7P22.1) MUTATED	46	16	13	45	15	39
AMP PEAK 10(7P22.1) WILD-TYPE	38	41	22	31	13	22

Figure S82. 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 = 3.8e-05

Table S83. Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 11(7P11.2) MUTATED	74	48	35	46	11
AMP PEAK 11(7P11.2) WILD-TYPE	49	139	1	30	8

Figure S83. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 11(7P11.2) MUTATED	76	64	19	32
AMP PEAK 11(7P11.2) WILD-TYPE	48	57	23	74

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

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.058

Table S85. Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 11(7P11.2) MUTATED	26	24	14	22	37
AMP PEAK 11(7P11.2) WILD-TYPE	36	38	30	18	27

Figure S85. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00767 (Fisher's exact test), Q value = 0.014

Table S86. Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 11(7P11.2) MUTATED	81	51	77
AMP PEAK 11(7P11.2) WILD-TYPE	91	79	55

Figure S86. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0017

Table S87. 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 S87. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0026

Table S88. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 11(7P11.2) MUTATED	45	14	12	41	14	35
AMP PEAK 11(7P11.2) WILD-TYPE	39	43	23	35	14	26

Figure S88. 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 = 3.8e-05

Table S89. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 12(7Q21.2) MUTATED	63	50	36	43	12
AMP PEAK 12(7Q21.2) WILD-TYPE	60	137	0	33	7

Figure S89. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 12(7Q21.2) MUTATED	74	54	20	31
AMP PEAK 12(7Q21.2) WILD-TYPE	50	67	22	75

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

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.044

Table S91. Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 12(7Q21.2) MUTATED	82	48	70
AMP PEAK 12(7Q21.2) WILD-TYPE	90	82	62

Figure S91. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00684 (Fisher's exact test), Q value = 0.012

Table S92. 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 S92. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00889 (Fisher's exact test), Q value = 0.016

Table S93. Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 12(7Q21.2) MUTATED	40	14	12	39	14	33
AMP PEAK 12(7Q21.2) WILD-TYPE	44	43	23	37	14	28

Figure S93. 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 = 3.8e-05

Table S94. Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 13(7Q22.1) MUTATED	62	51	36	40	13
AMP PEAK 13(7Q22.1) WILD-TYPE	61	136	0	36	6

Figure S94. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0017

Table S95. Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 13(7Q22.1) MUTATED	71	55	20	32
AMP PEAK 13(7Q22.1) WILD-TYPE	53	66	22	74

Figure S95. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.048

Table S96. 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 S96. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00564 (Fisher's exact test), Q value = 0.01

Table S97. Gene #13: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 13(7Q22.1) MUTATED	42	15	10	40	15	31
AMP PEAK 13(7Q22.1) WILD-TYPE	42	42	25	36	13	30

Figure S97. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

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

Table S98. Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 14(8P23.1) MUTATED	36	82	15	25	19
AMP PEAK 14(8P23.1) WILD-TYPE	87	105	21	51	0

Figure S98. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00036

Table S99. Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 14(8P23.1) MUTATED	36	67	16	35
AMP PEAK 14(8P23.1) WILD-TYPE	88	54	26	71

Figure S99. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00278 (Fisher's exact test), Q value = 0.0054

Table S100. Gene #14: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 14(8P23.1) MUTATED	30	25	52
AMP PEAK 14(8P23.1) WILD-TYPE	80	32	53

Figure S100. Get High-res Image Gene #14: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

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

Table S101. Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 15(8Q24.21) MUTATED	111	107	24	49	18
AMP PEAK 15(8Q24.21) WILD-TYPE	12	80	12	27	1

Figure S101. 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 = 3.8e-05

Table S102. Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 15(8Q24.21) MUTATED	103	92	18	59
AMP PEAK 15(8Q24.21) WILD-TYPE	21	29	24	47

Figure S102. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0058

Table S103. Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 15(8Q24.21) MUTATED	40	35	22	25	53
AMP PEAK 15(8Q24.21) WILD-TYPE	22	27	22	15	11

Figure S103. 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 = 3.8e-05

Table S104. Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 15(8Q24.21) MUTATED	121	72	112
AMP PEAK 15(8Q24.21) WILD-TYPE	51	58	20

Figure S104. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 5e-04

Table S105. 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 S105. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00039

Table S106. Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 15(8Q24.21) MUTATED	62	46	41	38	21	29
AMP PEAK 15(8Q24.21) WILD-TYPE	11	11	18	22	12	30

Figure S106. 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 = 0.00026 (Fisher's exact test), Q value = 0.00066

Table S107. Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 15(8Q24.21) MUTATED	62	28	22	55	17	53
AMP PEAK 15(8Q24.21) WILD-TYPE	22	29	13	21	11	8

Figure S107. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S108. Gene #16: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 16(9P24.1) MUTATED	30	29	3	1	2
AMP PEAK 16(9P24.1) WILD-TYPE	93	158	33	75	17

Figure S108. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00196 (Fisher's exact test), Q value = 0.004

Table S109. Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 16(9P24.1) MUTATED	26	2	16
AMP PEAK 16(9P24.1) WILD-TYPE	84	55	89

Figure S109. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.055

Table S110. Gene #16: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 16(9P24.1) MUTATED	23	13	28
AMP PEAK 16(9P24.1) WILD-TYPE	149	117	104

Figure S110. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p13.2' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00086

Table S111. Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 17(9P13.2) MUTATED	43	28	5	11	4
AMP PEAK 17(9P13.2) WILD-TYPE	80	159	31	65	15

Figure S111. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 0.063

Table S112. 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 S112. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_9p13.2' versus 'MRNASEQ_CNMF'

P value = 0.048 (Fisher's exact test), Q value = 0.07

Table S113. Gene #17: 'amp_9p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 17(9P13.2) MUTATED	10	4	11	9	14
AMP PEAK 17(9P13.2) WILD-TYPE	52	58	33	31	50

Figure S113. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0459 (Fisher's exact test), Q value = 0.067

Table S114. Gene #17: 'amp_9p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 17(9P13.2) MUTATED	23	4	21
AMP PEAK 17(9P13.2) WILD-TYPE	87	53	84

Figure S114. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0418 (Fisher's exact test), Q value = 0.062

Table S115. Gene #17: 'amp_9p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 17(9P13.2) MUTATED	34	19	36
AMP PEAK 17(9P13.2) WILD-TYPE	138	111	96

Figure S115. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0017

Table S116. Gene #17: 'amp_9p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 17(9P13.2) MUTATED	27	15	9	12	3	5
AMP PEAK 17(9P13.2) WILD-TYPE	46	42	50	48	30	54

Figure S116. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

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

Table S117. Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 18(9Q34.3) MUTATED	52	31	13	19	7
AMP PEAK 18(9Q34.3) WILD-TYPE	71	156	23	57	12

Figure S117. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.022

Table S118. Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 18(9Q34.3) MUTATED	47	32	7	23
AMP PEAK 18(9Q34.3) WILD-TYPE	77	89	35	83

Figure S118. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

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

Table S119. Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 18(9Q34.3) MUTATED	13	6	10	11	23
AMP PEAK 18(9Q34.3) WILD-TYPE	49	56	34	29	41

Figure S119. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S120. Gene #18: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 18(9Q34.3) MUTATED	30	5	28
AMP PEAK 18(9Q34.3) WILD-TYPE	80	52	77

Figure S120. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 18(9Q34.3) MUTATED	44	27	49
AMP PEAK 18(9Q34.3) WILD-TYPE	128	103	83

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

'amp_9q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.0087

Table S122. Gene #18: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 18(9Q34.3) MUTATED	26	11	4	28	2	17
AMP PEAK 18(9Q34.3) WILD-TYPE	58	46	31	48	26	44

Figure S122. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p11.22' versus 'CN_CNMF'

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

Table S123. Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 19(10P11.22) MUTATED	53	12	14	36	4
AMP PEAK 19(10P11.22) WILD-TYPE	70	175	22	40	15

Figure S123. 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 = 3.8e-05

Table S124. Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 19(10P11.22) MUTATED	55	30	3	19
AMP PEAK 19(10P11.22) WILD-TYPE	69	91	39	87

Figure S124. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.005

Table S125. Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 19(10P11.22) MUTATED	11	12	8	10	29
AMP PEAK 19(10P11.22) WILD-TYPE	51	50	36	30	35

Figure S125. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0027

Table S126. Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 19(10P11.22) MUTATED	39	26	51
AMP PEAK 19(10P11.22) WILD-TYPE	133	104	81

Figure S126. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S127. 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 S127. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.0065

Table S128. Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 19(10P11.22) MUTATED	32	16	8	14	10	12
AMP PEAK 19(10P11.22) WILD-TYPE	41	41	51	46	23	47

Figure S128. 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 = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S129. Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 19(10P11.22) MUTATED	27	6	4	23	4	28
AMP PEAK 19(10P11.22) WILD-TYPE	57	51	31	53	24	33

Figure S129. 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 = 3.8e-05

Table S130. Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 20(10Q22.2) MUTATED	27	11	6	37	7
AMP PEAK 20(10Q22.2) WILD-TYPE	96	176	30	39	12

Figure S130. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'METHLYATION_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.06

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 20(10Q22.2) MUTATED	31	29	4	15
AMP PEAK 20(10Q22.2) WILD-TYPE	93	92	38	91

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

'amp_10q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.059

Table S132. Gene #20: 'amp_10q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 20(10Q22.2) MUTATED	8	10	10	5	21
AMP PEAK 20(10Q22.2) WILD-TYPE	54	52	34	35	43

Figure S132. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0354 (Fisher's exact test), Q value = 0.054

Table S133. Gene #20: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 20(10Q22.2) MUTATED	30	7	17
AMP PEAK 20(10Q22.2) WILD-TYPE	80	50	88

Figure S133. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.017

Table S134. Gene #20: 'amp_10q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 20(10Q22.2) MUTATED	16	8	3	25	2	15
AMP PEAK 20(10Q22.2) WILD-TYPE	68	49	32	51	26	46

Figure S134. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q26.13' versus 'CN_CNMF'

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

Table S135. Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 21(10Q26.13) MUTATED	31	14	8	30	5
AMP PEAK 21(10Q26.13) WILD-TYPE	92	173	28	46	14

Figure S135. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00041

Table S136. Gene #21: 'amp_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 21(10Q26.13) MUTATED	40	18	3	14
AMP PEAK 21(10Q26.13) WILD-TYPE	84	103	39	92

Figure S136. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CNMF'

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

Table S137. Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 21(10Q26.13) MUTATED	8	14	5	5	22
AMP PEAK 21(10Q26.13) WILD-TYPE	54	48	39	35	42

Figure S137. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.058

Table S138. Gene #21: 'amp_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 21(10Q26.13) MUTATED	20	9	4	19	1	17
AMP PEAK 21(10Q26.13) WILD-TYPE	64	48	31	57	27	44

Figure S138. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

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

Table S139. Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 22(11P13) MUTATED	42	17	3	24	2
AMP PEAK 22(11P13) WILD-TYPE	81	170	33	52	17

Figure S139. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

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

Table S140. Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 22(11P13) MUTATED	40	13	7	19
AMP PEAK 22(11P13) WILD-TYPE	84	108	35	87

Figure S140. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0018

Table S141. Gene #22: 'amp_11p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 22(11P13) MUTATED	7	14	5	1	20
AMP PEAK 22(11P13) WILD-TYPE	55	48	39	39	44

Figure S141. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S142. Gene #22: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 22(11P13) MUTATED	32	10	5
AMP PEAK 22(11P13) WILD-TYPE	78	47	100

Figure S142. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0016

Table S143. Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 22(11P13) MUTATED	24	21	41
AMP PEAK 22(11P13) WILD-TYPE	148	109	91

Figure S143. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S144. 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 S144. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.0057

Table S145. Gene #22: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 22(11P13) MUTATED	12	9	6	14	2	24
AMP PEAK 22(11P13) WILD-TYPE	72	48	29	62	26	37

Figure S145. 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 = 3.8e-05

Table S146. Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 23(11P11.2) MUTATED	47	10	5	28	2
AMP PEAK 23(11P11.2) WILD-TYPE	76	177	31	48	17

Figure S146. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 23(11P11.2) MUTATED	46	16	6	13
AMP PEAK 23(11P11.2) WILD-TYPE	78	105	36	93

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

'amp_11p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0391 (Fisher's exact test), Q value = 0.059

Table S148. 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 S148. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S149. Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 23(11P11.2) MUTATED	6	7	5	2	25
AMP PEAK 23(11P11.2) WILD-TYPE	56	55	39	38	39

Figure S149. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S150. Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 23(11P11.2) MUTATED	32	4	9
AMP PEAK 23(11P11.2) WILD-TYPE	78	53	96

Figure S150. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

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

Table S151. Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 23(11P11.2) MUTATED	30	13	46
AMP PEAK 23(11P11.2) WILD-TYPE	142	117	86

Figure S151. 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 = 3.8e-05

Table S152. 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 S152. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0016

Table S153. Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 23(11P11.2) MUTATED	27	14	6	8	7	6
AMP PEAK 23(11P11.2) WILD-TYPE	46	43	53	52	26	53

Figure S153. 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 = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S154. Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 23(11P11.2) MUTATED	17	3	5	16	2	25
AMP PEAK 23(11P11.2) WILD-TYPE	67	54	30	60	26	36

Figure S154. 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 = 3.8e-05

Table S155. Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 24(11Q13.3) MUTATED	50	16	5	36	8
AMP PEAK 24(11Q13.3) WILD-TYPE	73	171	31	40	11

Figure S155. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00382 (Fisher's exact test), Q value = 0.0072

Table S156. Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 24(11Q13.3) MUTATED	46	30	6	20
AMP PEAK 24(11Q13.3) WILD-TYPE	78	91	36	86

Figure S156. 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 = 0.064

Table S157. 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 S157. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.048

Table S158. Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 24(11Q13.3) MUTATED	33	8	19
AMP PEAK 24(11Q13.3) WILD-TYPE	77	49	86

Figure S158. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

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

Table S159. Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 24(11Q13.3) MUTATED	42	18	52
AMP PEAK 24(11Q13.3) WILD-TYPE	130	112	80

Figure S159. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.00088

Table S160. 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 S160. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.003

Table S161. Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 24(11Q13.3) MUTATED	26	20	7	16	12	8
AMP PEAK 24(11Q13.3) WILD-TYPE	47	37	52	44	21	51

Figure S161. 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 = 0.00041 (Fisher's exact test), Q value = 0.00099

Table S162. Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 24(11Q13.3) MUTATED	22	6	4	29	5	23
AMP PEAK 24(11Q13.3) WILD-TYPE	62	51	31	47	23	38

Figure S162. 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 = 3.8e-05

Table S163. Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 25(12P12.1) MUTATED	39	26	13	42	8
AMP PEAK 25(12P12.1) WILD-TYPE	84	161	23	34	11

Figure S163. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.048

Table S164. Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 25(12P12.1) MUTATED	48	37	12	22
AMP PEAK 25(12P12.1) WILD-TYPE	76	84	30	84

Figure S164. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00651 (Fisher's exact test), Q value = 0.012

Table S165. Gene #25: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 25(12P12.1) MUTATED	45	29	52
AMP PEAK 25(12P12.1) WILD-TYPE	127	101	80

Figure S165. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.06

Table S166. Gene #25: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 25(12P12.1) MUTATED	28	9	6	26	9	23
AMP PEAK 25(12P12.1) WILD-TYPE	56	48	29	50	19	38

Figure S166. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

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

Table S167. Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 26(12Q15) MUTATED	32	24	7	41	5
AMP PEAK 26(12Q15) WILD-TYPE	91	163	29	35	14

Figure S167. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.0193 (Fisher's exact test), Q value = 0.032

Table S168. Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 26(12Q15) MUTATED	39	22	15	21
AMP PEAK 26(12Q15) WILD-TYPE	85	99	27	85

Figure S168. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'RPPA_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.029

Table S169. 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 S169. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.041

Table S170. Gene #26: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 26(12Q15) MUTATED	34	7	25
AMP PEAK 26(12Q15) WILD-TYPE	76	50	80

Figure S170. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'CN_CNMF'

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

Table S171. Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 27(13Q12.3) MUTATED	79	35	27	19	10
AMP PEAK 27(13Q12.3) WILD-TYPE	44	152	9	57	9

Figure S171. 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 = 3.8e-05

Table S172. Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 27(13Q12.3) MUTATED	74	39	8	30
AMP PEAK 27(13Q12.3) WILD-TYPE	50	82	34	76

Figure S172. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

P value = 0.0079 (Fisher's exact test), Q value = 0.014

Table S173. Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 27(13Q12.3) MUTATED	19	17	12	21	32
AMP PEAK 27(13Q12.3) WILD-TYPE	43	45	32	19	32

Figure S173. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S174. Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 27(13Q12.3) MUTATED	56	39	72
AMP PEAK 27(13Q12.3) WILD-TYPE	116	91	60

Figure S174. 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 = 0.00031

Table S175. 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 S175. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.0066

Table S176. Gene #27: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 27(13Q12.3) MUTATED	38	16	21	22	18	14
AMP PEAK 27(13Q12.3) WILD-TYPE	35	41	38	38	15	45

Figure S176. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0014

Table S177. Gene #27: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 27(13Q12.3) MUTATED	30	15	10	29	7	38
AMP PEAK 27(13Q12.3) WILD-TYPE	54	42	25	47	21	23

Figure S177. 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 = 3.8e-05

Table S178. Gene #28: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 28(13Q22.1) MUTATED	89	40	25	20	7
AMP PEAK 28(13Q22.1) WILD-TYPE	34	147	11	56	12

Figure S178. 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 = 3.8e-05

Table S179. Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 28(13Q22.1) MUTATED	79	39	10	31
AMP PEAK 28(13Q22.1) WILD-TYPE	45	82	32	75

Figure S179. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S180. Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 28(13Q22.1) MUTATED	20	16	9	20	38
AMP PEAK 28(13Q22.1) WILD-TYPE	42	46	35	20	26

Figure S180. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

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

Table S181. Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 28(13Q22.1) MUTATED	59	38	80
AMP PEAK 28(13Q22.1) WILD-TYPE	113	92	52

Figure S181. 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 = 3.8e-05

Table S182. 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 S182. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00026

Table S183. Gene #28: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 28(13Q22.1) MUTATED	45	20	23	20	17	13
AMP PEAK 28(13Q22.1) WILD-TYPE	28	37	36	40	16	46

Figure S183. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S184. Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 28(13Q22.1) MUTATED	35	14	11	30	7	41
AMP PEAK 28(13Q22.1) WILD-TYPE	49	43	24	46	21	20

Figure S184. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

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

Table S185. Gene #29: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 29(15Q26.1) MUTATED	61	15	5	31	1
AMP PEAK 29(15Q26.1) WILD-TYPE	62	172	31	45	18

Figure S185. Get High-res Image Gene #29: '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 = 3.8e-05

Table S186. Gene #29: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 29(15Q26.1) MUTATED	57	29	1	15
AMP PEAK 29(15Q26.1) WILD-TYPE	67	92	41	91

Figure S186. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

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

Table S187. Gene #29: '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 29(15Q26.1) MUTATED	46	12	22	11
AMP PEAK 29(15Q26.1) WILD-TYPE	94	46	56	69

Figure S187. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S188. Gene #29: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 29(15Q26.1) MUTATED	12	4	10	11	28
AMP PEAK 29(15Q26.1) WILD-TYPE	50	58	34	29	36

Figure S188. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0023

Table S189. Gene #29: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 29(15Q26.1) MUTATED	37	5	23
AMP PEAK 29(15Q26.1) WILD-TYPE	73	52	82

Figure S189. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S190. Gene #29: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 29(15Q26.1) MUTATED	46	18	47
AMP PEAK 29(15Q26.1) WILD-TYPE	126	112	85

Figure S190. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S191. Gene #29: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 29(15Q26.1) MUTATED	61	8	42
AMP PEAK 29(15Q26.1) WILD-TYPE	182	74	67

Figure S191. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S192. Gene #29: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 29(15Q26.1) MUTATED	29	14	20	19	5	6
AMP PEAK 29(15Q26.1) WILD-TYPE	44	43	39	41	28	53

Figure S192. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S193. Gene #29: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 29(15Q26.1) MUTATED	30	3	7	27	2	24
AMP PEAK 29(15Q26.1) WILD-TYPE	54	54	28	49	26	37

Figure S193. Get High-res Image Gene #29: '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 = 3.8e-05

Table S194. Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 30(17Q12) MUTATED	82	21	14	23	7
AMP PEAK 30(17Q12) WILD-TYPE	41	166	22	53	12

Figure S194. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

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

Table S195. Gene #30: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 30(17Q12) MUTATED	69	33	12	19
AMP PEAK 30(17Q12) WILD-TYPE	55	88	30	87

Figure S195. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

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

Table S196. Gene #30: '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 30(17Q12) MUTATED	16	37	24	22	14
AMP PEAK 30(17Q12) WILD-TYPE	14	55	58	71	45

Figure S196. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S197. Gene #30: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
AMP PEAK 30(17Q12) MUTATED	55	7	33	18
AMP PEAK 30(17Q12) WILD-TYPE	85	51	45	62

Figure S197. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S198. Gene #30: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 30(17Q12) MUTATED	14	10	13	8	34
AMP PEAK 30(17Q12) WILD-TYPE	48	52	31	32	30

Figure S198. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S199. Gene #30: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 30(17Q12) MUTATED	49	7	23
AMP PEAK 30(17Q12) WILD-TYPE	61	50	82

Figure S199. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

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

Table S200. Gene #30: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 30(17Q12) MUTATED	43	28	73
AMP PEAK 30(17Q12) WILD-TYPE	129	102	59

Figure S200. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S201. Gene #30: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 30(17Q12) MUTATED	71	16	57
AMP PEAK 30(17Q12) WILD-TYPE	172	66	52

Figure S201. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.0061

Table S202. Gene #30: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 30(17Q12) MUTATED	38	16	18	20	10	11
AMP PEAK 30(17Q12) WILD-TYPE	35	41	41	40	23	48

Figure S202. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S203. Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 30(17Q12) MUTATED	32	8	6	33	5	29
AMP PEAK 30(17Q12) WILD-TYPE	52	49	29	43	23	32

Figure S203. Get High-res Image Gene #30: '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 = 3.8e-05

Table S204. Gene #31: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 31(18Q11.2) MUTATED	58	27	12	36	7
AMP PEAK 31(18Q11.2) WILD-TYPE	65	160	24	40	12

Figure S204. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S205. Gene #31: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 31(18Q11.2) MUTATED	55	37	3	28
AMP PEAK 31(18Q11.2) WILD-TYPE	69	84	39	78

Figure S205. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.026

Table S206. Gene #31: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 31(18Q11.2) MUTATED	12	12	16	8	26
AMP PEAK 31(18Q11.2) WILD-TYPE	50	50	28	32	38

Figure S206. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

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

Table S207. Gene #31: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 31(18Q11.2) MUTATED	42	32	64
AMP PEAK 31(18Q11.2) WILD-TYPE	130	98	68

Figure S207. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00084

Table S208. Gene #31: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
AMP PEAK 31(18Q11.2) MUTATED	66	20	52
AMP PEAK 31(18Q11.2) WILD-TYPE	177	62	57

Figure S208. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00399 (Fisher's exact test), Q value = 0.0075

Table S209. Gene #31: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 31(18Q11.2) MUTATED	30	12	5	25	4	27
AMP PEAK 31(18Q11.2) WILD-TYPE	54	45	30	51	24	34

Figure S209. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S210. Gene #32: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 32(19P13.2) MUTATED	18	6	10	12	1
AMP PEAK 32(19P13.2) WILD-TYPE	105	181	26	64	18

Figure S210. Get High-res Image Gene #32: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

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

Table S211. Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 33(19Q12) MUTATED	79	17	10	23	1
AMP PEAK 33(19Q12) WILD-TYPE	44	170	26	53	18

Figure S211. 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 = 3.8e-05

Table S212. Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 33(19Q12) MUTATED	67	21	9	21
AMP PEAK 33(19Q12) WILD-TYPE	57	100	33	85

Figure S212. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00061

Table S213. 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 S213. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S214. 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 S214. 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 = 3.8e-05

Table S215. Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 33(19Q12) MUTATED	10	9	8	6	46
AMP PEAK 33(19Q12) WILD-TYPE	52	53	36	34	18

Figure S215. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S216. Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 33(19Q12) MUTATED	53	6	20
AMP PEAK 33(19Q12) WILD-TYPE	57	51	85

Figure S216. 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 = 3.8e-05

Table S217. Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 33(19Q12) MUTATED	32	27	70
AMP PEAK 33(19Q12) WILD-TYPE	140	103	62

Figure S217. 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 = 3.8e-05

Table S218. 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 S218. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S219. Gene #33: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 33(19Q12) MUTATED	41	11	15	12	12	13
AMP PEAK 33(19Q12) WILD-TYPE	32	46	44	48	21	46

Figure S219. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S220. Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 33(19Q12) MUTATED	24	9	7	16	6	42
AMP PEAK 33(19Q12) WILD-TYPE	60	48	28	60	22	19

Figure S220. 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 = 3.8e-05

Table S221. Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 34(19Q13.32) MUTATED	55	20	11	25	0
AMP PEAK 34(19Q13.32) WILD-TYPE	68	167	25	51	19

Figure S221. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.32' versus 'METHLYATION_CNMF'

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

Table S222. Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 34(19Q13.32) MUTATED	43	25	12	18
AMP PEAK 34(19Q13.32) WILD-TYPE	81	96	30	88

Figure S222. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.02

Table S223. 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 S223. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q13.32' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S224. Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 34(19Q13.32) MUTATED	13	8	8	6	30
AMP PEAK 34(19Q13.32) WILD-TYPE	49	54	36	34	34

Figure S224. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.013

Table S225. Gene #34: 'amp_19q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 34(19Q13.32) MUTATED	37	8	20
AMP PEAK 34(19Q13.32) WILD-TYPE	73	49	85

Figure S225. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.002

Table S226. Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 34(19Q13.32) MUTATED	36	25	49
AMP PEAK 34(19Q13.32) WILD-TYPE	136	105	83

Figure S226. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S227. 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 S227. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S228. Gene #34: 'amp_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 34(19Q13.32) MUTATED	29	12	9	14	10	9
AMP PEAK 34(19Q13.32) WILD-TYPE	44	45	50	46	23	50

Figure S228. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.0033

Table S229. Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 34(19Q13.32) MUTATED	16	7	5	20	9	26
AMP PEAK 34(19Q13.32) WILD-TYPE	68	50	30	56	19	35

Figure S229. 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 = 3.8e-05

Table S230. Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 35(20Q13.2) MUTATED	116	69	32	60	16
AMP PEAK 35(20Q13.2) WILD-TYPE	7	118	4	16	3

Figure S230. 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 = 3.8e-05

Table S231. Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 35(20Q13.2) MUTATED	118	60	32	51
AMP PEAK 35(20Q13.2) WILD-TYPE	6	61	10	55

Figure S231. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.045

Table S232. 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 S232. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

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

Table S233. 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 S233. 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 = 3.8e-05

Table S234. Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
AMP PEAK 35(20Q13.2) MUTATED	29	31	29	26	61
AMP PEAK 35(20Q13.2) WILD-TYPE	33	31	15	14	3

Figure S234. 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 = 3.8e-05

Table S235. Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
AMP PEAK 35(20Q13.2) MUTATED	91	25	60
AMP PEAK 35(20Q13.2) WILD-TYPE	19	32	45

Figure S235. 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 = 3.8e-05

Table S236. Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 35(20Q13.2) MUTATED	98	72	118
AMP PEAK 35(20Q13.2) WILD-TYPE	74	58	14

Figure S236. 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 = 3.8e-05

Table S237. 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 S237. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S238. Gene #35: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
AMP PEAK 35(20Q13.2) MUTATED	62	30	37	37	25	30
AMP PEAK 35(20Q13.2) WILD-TYPE	11	27	22	23	8	29

Figure S238. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S239. Gene #35: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 35(20Q13.2) MUTATED	57	27	20	44	16	57
AMP PEAK 35(20Q13.2) WILD-TYPE	27	30	15	32	12	4

Figure S239. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq27.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S240. Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
AMP PEAK 36(XQ27.3) MUTATED	32	17	13	19	5
AMP PEAK 36(XQ27.3) WILD-TYPE	91	170	23	57	14

Figure S240. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'METHLYATION_CNMF'

P value = 0.00836 (Fisher's exact test), Q value = 0.015

Table S241. Gene #36: 'amp_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
AMP PEAK 36(XQ27.3) MUTATED	26	32	7	10
AMP PEAK 36(XQ27.3) WILD-TYPE	98	89	35	96

Figure S241. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq27.3' versus 'MIRSEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.066

Table S242. Gene #36: 'amp_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
AMP PEAK 36(XQ27.3) MUTATED	38	16	30
AMP PEAK 36(XQ27.3) WILD-TYPE	134	114	102

Figure S242. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 0.057

Table S243. Gene #36: 'amp_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
AMP PEAK 36(XQ27.3) MUTATED	20	3	7	19	5	10
AMP PEAK 36(XQ27.3) WILD-TYPE	64	54	28	57	23	51

Figure S243. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

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

Table S244. Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 1(1P36.11) MUTATED	73	12	5	39	6
DEL PEAK 1(1P36.11) WILD-TYPE	50	175	31	37	13

Figure S244. 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 = 3.8e-05

Table S245. Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 1(1P36.11) MUTATED	69	26	4	18
DEL PEAK 1(1P36.11) WILD-TYPE	55	95	38	88

Figure S245. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.0033

Table S246. 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 S246. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S247. 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 S247. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00029

Table S248. Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 1(1P36.11) MUTATED	12	7	16	11	30
DEL PEAK 1(1P36.11) WILD-TYPE	50	55	28	29	34

Figure S248. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00245 (Fisher's exact test), Q value = 0.0049

Table S249. Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 1(1P36.11) MUTATED	41	7	28
DEL PEAK 1(1P36.11) WILD-TYPE	69	50	77

Figure S249. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S250. Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 1(1P36.11) MUTATED	48	24	60
DEL PEAK 1(1P36.11) WILD-TYPE	124	106	72

Figure S250. 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 = 3.8e-05

Table S251. 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 S251. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

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

Table S252. Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 1(1P36.11) MUTATED	41	12	18	15	9	8
DEL PEAK 1(1P36.11) WILD-TYPE	32	45	41	45	24	51

Figure S252. 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 = 3.8e-05

Table S253. Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 1(1P36.11) MUTATED	31	5	8	21	5	33
DEL PEAK 1(1P36.11) WILD-TYPE	53	52	27	55	23	28

Figure S253. 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 = 3.8e-05

Table S254. Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 2(1P13.2) MUTATED	57	7	7	19	4
DEL PEAK 2(1P13.2) WILD-TYPE	66	180	29	57	15

Figure S254. 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 = 3.8e-05

Table S255. Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 2(1P13.2) MUTATED	50	21	6	8
DEL PEAK 2(1P13.2) WILD-TYPE	74	100	36	98

Figure S255. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'RPPA_CNMF'

P value = 0.0058 (Fisher's exact test), Q value = 0.011

Table S256. 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	11	20
DEL PEAK 2(1P13.2) WILD-TYPE	24	76	58	82	39

Figure S256. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

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

Table S257. Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 2(1P13.2) MUTATED	8	5	5	8	23
DEL PEAK 2(1P13.2) WILD-TYPE	54	57	39	32	41

Figure S257. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00964 (Fisher's exact test), Q value = 0.017

Table S258. Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 2(1P13.2) MUTATED	29	5	15
DEL PEAK 2(1P13.2) WILD-TYPE	81	52	90

Figure S258. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0016

Table S259. Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 2(1P13.2) MUTATED	33	17	42
DEL PEAK 2(1P13.2) WILD-TYPE	139	113	90

Figure S259. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00268 (Fisher's exact test), Q value = 0.0052

Table S260. 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	49	9	34
DEL PEAK 2(1P13.2) WILD-TYPE	194	73	75

Figure S260. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 5e-04

Table S261. Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 2(1P13.2) MUTATED	19	4	3	17	5	25
DEL PEAK 2(1P13.2) WILD-TYPE	65	53	32	59	23	36

Figure S261. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0011

Table S262. Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 3(1Q44) MUTATED	13	3	6	6	2
DEL PEAK 3(1Q44) WILD-TYPE	110	184	30	70	17

Figure S262. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0038

Table S263. Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 3(1Q44) MUTATED	16	6	3	1
DEL PEAK 3(1Q44) WILD-TYPE	108	115	39	105

Figure S263. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.033

Table S264. Gene #39: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 3(1Q44) MUTATED	12	3	14
DEL PEAK 3(1Q44) WILD-TYPE	160	127	118

Figure S264. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'CN_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.005

Table S265. Gene #40: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 4(1Q44) MUTATED	11	3	4	5	3
DEL PEAK 4(1Q44) WILD-TYPE	112	184	32	71	16

Figure S265. Get High-res Image Gene #40: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0043

Table S266. Gene #40: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 4(1Q44) MUTATED	16	7	2	1
DEL PEAK 4(1Q44) WILD-TYPE	108	114	40	105

Figure S266. Get High-res Image Gene #40: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 9e-04

Table S267. Gene #41: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 5(2Q32.1) MUTATED	28	12	7	15	2
DEL PEAK 5(2Q32.1) WILD-TYPE	95	175	29	61	17

Figure S267. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00099

Table S268. Gene #41: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 5(2Q32.1) MUTATED	29	18	1	8
DEL PEAK 5(2Q32.1) WILD-TYPE	95	103	41	98

Figure S268. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MIRSEQ_CNMF'

P value = 0.00485 (Fisher's exact test), Q value = 0.009

Table S269. Gene #41: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 5(2Q32.1) MUTATED	16	17	30
DEL PEAK 5(2Q32.1) WILD-TYPE	156	113	102

Figure S269. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 9e-04

Table S270. Gene #41: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 5(2Q32.1) MUTATED	24	10	29
DEL PEAK 5(2Q32.1) WILD-TYPE	219	72	80

Figure S270. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00057

Table S271. Gene #42: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 6(2Q33.3) MUTATED	24	8	7	9	1
DEL PEAK 6(2Q33.3) WILD-TYPE	99	179	29	67	18

Figure S271. Get High-res Image Gene #42: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.033

Table S272. Gene #42: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 6(2Q33.3) MUTATED	16	9	23
DEL PEAK 6(2Q33.3) WILD-TYPE	156	121	109

Figure S272. Get High-res Image Gene #42: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00446 (Fisher's exact test), Q value = 0.0083

Table S273. Gene #42: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 6(2Q33.3) MUTATED	25	3	20
DEL PEAK 6(2Q33.3) WILD-TYPE	218	79	89

Figure S273. Get High-res Image Gene #42: '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 = 3.8e-05

Table S274. Gene #43: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 7(2Q37.2) MUTATED	36	10	4	15	7
DEL PEAK 7(2Q37.2) WILD-TYPE	87	177	32	61	12

Figure S274. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S275. Gene #43: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 7(2Q37.2) MUTATED	38	14	1	14
DEL PEAK 7(2Q37.2) WILD-TYPE	86	107	41	92

Figure S275. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.0073

Table S276. Gene #43: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 7(2Q37.2) MUTATED	3	6	10	6	17
DEL PEAK 7(2Q37.2) WILD-TYPE	59	56	34	34	47

Figure S276. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00041

Table S277. Gene #43: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 7(2Q37.2) MUTATED	20	14	37
DEL PEAK 7(2Q37.2) WILD-TYPE	152	116	95

Figure S277. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S278. Gene #43: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 7(2Q37.2) MUTATED	32	6	33
DEL PEAK 7(2Q37.2) WILD-TYPE	211	76	76

Figure S278. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 0.015

Table S279. Gene #43: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 7(2Q37.2) MUTATED	20	4	3	12	3	18
DEL PEAK 7(2Q37.2) WILD-TYPE	64	53	32	64	25	43

Figure S279. Get High-res Image Gene #43: '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 = 3.8e-05

Table S280. Gene #44: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 8(3P26.1) MUTATED	65	19	16	36	7
DEL PEAK 8(3P26.1) WILD-TYPE	58	168	20	40	12

Figure S280. Get High-res Image Gene #44: '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 = 3.8e-05

Table S281. Gene #44: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 8(3P26.1) MUTATED	67	33	9	20
DEL PEAK 8(3P26.1) WILD-TYPE	57	88	33	86

Figure S281. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CNMF'

P value = 0.00807 (Fisher's exact test), Q value = 0.014

Table S282. Gene #44: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 8(3P26.1) MUTATED	11	11	12	14	27
DEL PEAK 8(3P26.1) WILD-TYPE	51	51	32	26	37

Figure S282. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CNMF'

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

Table S283. Gene #44: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 8(3P26.1) MUTATED	46	29	65
DEL PEAK 8(3P26.1) WILD-TYPE	126	101	67

Figure S283. Get High-res Image Gene #44: '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 = 3.8e-05

Table S284. Gene #44: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 8(3P26.1) MUTATED	66	16	58
DEL PEAK 8(3P26.1) WILD-TYPE	177	66	51

Figure S284. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0035

Table S285. Gene #44: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 8(3P26.1) MUTATED	37	18	13	16	14	13
DEL PEAK 8(3P26.1) WILD-TYPE	36	39	46	44	19	46

Figure S285. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S286. Gene #44: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 8(3P26.1) MUTATED	25	9	7	27	7	36
DEL PEAK 8(3P26.1) WILD-TYPE	59	48	28	49	21	25

Figure S286. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

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

Table S287. Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 9(3P14.2) MUTATED	67	28	16	37	10
DEL PEAK 9(3P14.2) WILD-TYPE	56	159	20	39	9

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 = 3.8e-05

Table S288. Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 9(3P14.2) MUTATED	70	41	15	19
DEL PEAK 9(3P14.2) WILD-TYPE	54	80	27	87

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 = 6e-05 (Fisher's exact test), Q value = 0.00018

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	62	62	44	40	64
DEL PEAK 9(3P14.2) MUTATED	16	9	14	14	35
DEL PEAK 9(3P14.2) WILD-TYPE	46	53	30	26	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 = 0.00365 (Fisher's exact test), Q value = 0.0069

Table S290. Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 9(3P14.2) MUTATED	45	9	34
DEL PEAK 9(3P14.2) WILD-TYPE	65	48	71

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

Table S291. Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 9(3P14.2) MUTATED	55	29	71
DEL PEAK 9(3P14.2) WILD-TYPE	117	101	61

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 = 3.8e-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	61
DEL PEAK 9(3P14.2) WILD-TYPE	165	66	48

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 = 0.0338 (Fisher's exact test), Q value = 0.052

Table S293. Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 9(3P14.2) MUTATED	37	21	21	20	11	13
DEL PEAK 9(3P14.2) WILD-TYPE	36	36	38	40	22	46

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 = 3.8e-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	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 9(3P14.2) MUTATED	35	7	11	30	5	35
DEL PEAK 9(3P14.2) WILD-TYPE	49	50	24	46	23	26

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 = 3.8e-05

Table S295. Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 10(3Q26.31) MUTATED	27	3	6	10	1
DEL PEAK 10(3Q26.31) WILD-TYPE	96	184	30	66	18

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 = 3.8e-05

Table S296. Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 10(3Q26.31) MUTATED	28	11	2	2
DEL PEAK 10(3Q26.31) WILD-TYPE	96	110	40	104

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 = 0.00027 (Fisher's exact test), Q value = 0.00068

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	62	62	44	40	64
DEL PEAK 10(3Q26.31) MUTATED	2	2	1	6	14
DEL PEAK 10(3Q26.31) WILD-TYPE	60	60	43	34	50

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 = 0.00854 (Fisher's exact test), Q value = 0.015

Table S298. Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 10(3Q26.31) MUTATED	17	1	7
DEL PEAK 10(3Q26.31) WILD-TYPE	93	56	98

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 = 3.8e-05

Table S299. Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 10(3Q26.31) MUTATED	9	7	30
DEL PEAK 10(3Q26.31) WILD-TYPE	163	123	102

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 = 0.00101 (Fisher's exact test), Q value = 0.0022

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	22
DEL PEAK 10(3Q26.31) WILD-TYPE	223	78	87

Figure S300. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.0069

Table S301. Gene #46: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 10(3Q26.31) MUTATED	16	5	3	4	6	2
DEL PEAK 10(3Q26.31) WILD-TYPE	57	52	56	56	27	57

Figure S301. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00551 (Fisher's exact test), Q value = 0.01

Table S302. Gene #46: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 10(3Q26.31) MUTATED	9	3	1	9	0	14
DEL PEAK 10(3Q26.31) WILD-TYPE	75	54	34	67	28	47

Figure S302. 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 = 3.8e-05

Table S303. Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 11(4P16.3) MUTATED	76	33	12	44	4
DEL PEAK 11(4P16.3) WILD-TYPE	47	154	24	32	15

Figure S303. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

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

Table S304. Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 11(4P16.3) MUTATED	70	39	6	35
DEL PEAK 11(4P16.3) WILD-TYPE	54	82	36	71

Figure S304. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S305. Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 11(4P16.3) MUTATED	11	23	14	12	38
DEL PEAK 11(4P16.3) WILD-TYPE	51	39	30	28	26

Figure S305. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.019

Table S306. Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 11(4P16.3) MUTATED	50	21	27
DEL PEAK 11(4P16.3) WILD-TYPE	60	36	78

Figure S306. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S307. Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 11(4P16.3) MUTATED	48	49	71
DEL PEAK 11(4P16.3) WILD-TYPE	124	81	61

Figure S307. 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 = 3.8e-05

Table S308. 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 S308. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0013

Table S309. Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 11(4P16.3) MUTATED	41	21	12	19	17	24
DEL PEAK 11(4P16.3) WILD-TYPE	32	36	47	41	16	35

Figure S309. 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 = 3.8e-05

Table S310. Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 11(4P16.3) MUTATED	27	21	3	28	8	47
DEL PEAK 11(4P16.3) WILD-TYPE	57	36	32	48	20	14

Figure S310. 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 = 3.8e-05

Table S311. Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 12(4Q22.1) MUTATED	83	30	17	55	8
DEL PEAK 12(4Q22.1) WILD-TYPE	40	157	19	21	11

Figure S311. 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 = 3.8e-05

Table S312. Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 12(4Q22.1) MUTATED	77	52	6	37
DEL PEAK 12(4Q22.1) WILD-TYPE	47	69	36	69

Figure S312. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

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

Table S313. Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 12(4Q22.1) MUTATED	18	21	19	19	37
DEL PEAK 12(4Q22.1) WILD-TYPE	44	41	25	21	27

Figure S313. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0026

Table S314. Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 12(4Q22.1) MUTATED	65	49	75
DEL PEAK 12(4Q22.1) WILD-TYPE	107	81	57

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 = 0.00023

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 = 2e-04 (Fisher's exact test), Q value = 0.00053

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	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 12(4Q22.1) MUTATED	39	18	8	33	8	40
DEL PEAK 12(4Q22.1) WILD-TYPE	45	39	27	43	20	21

Figure S316. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

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

Table S317. Gene #49: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 13(4Q34.3) MUTATED	88	31	14	59	8
DEL PEAK 13(4Q34.3) WILD-TYPE	35	156	22	17	11

Figure S317. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

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

Table S318. Gene #49: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 13(4Q34.3) MUTATED	86	49	4	42
DEL PEAK 13(4Q34.3) WILD-TYPE	38	72	38	64

Figure S318. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.023

Table S319. Gene #49: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 13(4Q34.3) MUTATED	74	17	38	32
DEL PEAK 13(4Q34.3) WILD-TYPE	66	41	40	48

Figure S319. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S320. Gene #49: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 13(4Q34.3) MUTATED	14	22	19	17	41
DEL PEAK 13(4Q34.3) WILD-TYPE	48	40	25	23	23

Figure S320. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CNMF'

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

Table S321. Gene #49: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 13(4Q34.3) MUTATED	63	47	88
DEL PEAK 13(4Q34.3) WILD-TYPE	109	83	44

Figure S321. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S322. Gene #49: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 13(4Q34.3) MUTATED	96	27	75
DEL PEAK 13(4Q34.3) WILD-TYPE	147	55	34

Figure S322. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0202 (Fisher's exact test), Q value = 0.033

Table S323. Gene #49: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 13(4Q34.3) MUTATED	46	25	21	26	18	23
DEL PEAK 13(4Q34.3) WILD-TYPE	27	32	38	34	15	36

Figure S323. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S324. Gene #49: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 13(4Q34.3) MUTATED	44	20	7	35	8	45
DEL PEAK 13(4Q34.3) WILD-TYPE	40	37	28	41	20	16

Figure S324. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

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

Table S325. Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 14(5Q12.1) MUTATED	92	16	11	41	10
DEL PEAK 14(5Q12.1) WILD-TYPE	31	171	25	35	9

Figure S325. 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 = 3.8e-05

Table S326. Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 14(5Q12.1) MUTATED	92	39	4	21
DEL PEAK 14(5Q12.1) WILD-TYPE	32	82	38	85

Figure S326. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S327. 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 S327. 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 = 3.8e-05

Table S328. Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 14(5Q12.1) MUTATED	17	4	11	15	44
DEL PEAK 14(5Q12.1) WILD-TYPE	45	58	33	25	20

Figure S328. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S329. Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 14(5Q12.1) MUTATED	52	6	33
DEL PEAK 14(5Q12.1) WILD-TYPE	58	51	72

Figure S329. 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 = 3.8e-05

Table S330. Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 14(5Q12.1) MUTATED	54	24	89
DEL PEAK 14(5Q12.1) WILD-TYPE	118	106	43

Figure S330. 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 = 3.8e-05

Table S331. 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 S331. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S332. Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 14(5Q12.1) MUTATED	49	23	21	21	14	11
DEL PEAK 14(5Q12.1) WILD-TYPE	24	34	38	39	19	48

Figure S332. 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 = 3.8e-05

Table S333. Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 14(5Q12.1) MUTATED	33	8	6	35	5	52
DEL PEAK 14(5Q12.1) WILD-TYPE	51	49	29	41	23	9

Figure S333. 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 = 3.8e-05

Table S334. Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 15(5Q23.2) MUTATED	90	12	11	35	10
DEL PEAK 15(5Q23.2) WILD-TYPE	33	175	25	41	9

Figure S334. 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 = 3.8e-05

Table S335. Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 15(5Q23.2) MUTATED	88	34	6	17
DEL PEAK 15(5Q23.2) WILD-TYPE	36	87	36	89

Figure S335. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.0017

Table S336. 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 S336. 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 = 3.8e-05

Table S337. Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 15(5Q23.2) MUTATED	15	3	9	13	43
DEL PEAK 15(5Q23.2) WILD-TYPE	47	59	35	27	21

Figure S337. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S338. Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 15(5Q23.2) MUTATED	47	5	31
DEL PEAK 15(5Q23.2) WILD-TYPE	63	52	74

Figure S338. 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 = 3.8e-05

Table S339. Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 15(5Q23.2) MUTATED	48	18	89
DEL PEAK 15(5Q23.2) WILD-TYPE	124	112	43

Figure S339. 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 = 3.8e-05

Table S340. 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 S340. 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 = 3.8e-05

Table S341. Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 15(5Q23.2) MUTATED	50	21	16	18	13	10
DEL PEAK 15(5Q23.2) WILD-TYPE	23	36	43	42	20	49

Figure S341. 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 = 3.8e-05

Table S342. Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 15(5Q23.2) MUTATED	34	7	5	30	6	46
DEL PEAK 15(5Q23.2) WILD-TYPE	50	50	30	46	22	15

Figure S342. 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 = 3.8e-05

Table S343. Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 16(6P25.3) MUTATED	51	21	8	30	5
DEL PEAK 16(6P25.3) WILD-TYPE	72	166	28	46	14

Figure S343. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

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

Table S344. Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 16(6P25.3) MUTATED	54	33	3	18
DEL PEAK 16(6P25.3) WILD-TYPE	70	88	39	88

Figure S344. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00023

Table S345. Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 16(6P25.3) MUTATED	7	5	13	7	25
DEL PEAK 16(6P25.3) WILD-TYPE	55	57	31	33	39

Figure S345. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.018

Table S346. Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 16(6P25.3) MUTATED	31	5	21
DEL PEAK 16(6P25.3) WILD-TYPE	79	52	84

Figure S346. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

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

Table S347. Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 16(6P25.3) MUTATED	34	23	56
DEL PEAK 16(6P25.3) WILD-TYPE	138	107	76

Figure S347. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S348. 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 S348. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00057

Table S349. Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 16(6P25.3) MUTATED	28	7	6	25	2	25
DEL PEAK 16(6P25.3) WILD-TYPE	56	50	29	51	26	36

Figure S349. 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 = 3.8e-05

Table S350. Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 17(6Q14.1) MUTATED	30	13	10	30	6
DEL PEAK 17(6Q14.1) WILD-TYPE	93	174	26	46	13

Figure S350. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00044

Table S351. Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 17(6Q14.1) MUTATED	41	20	3	15
DEL PEAK 17(6Q14.1) WILD-TYPE	83	101	39	91

Figure S351. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'MRNASEQ_CNMF'

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

Table S352. Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 17(6Q14.1) MUTATED	7	4	15	6	16
DEL PEAK 17(6Q14.1) WILD-TYPE	55	58	29	34	48

Figure S352. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.061

Table S353. Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 17(6Q14.1) MUTATED	21	4	23
DEL PEAK 17(6Q14.1) WILD-TYPE	89	53	82

Figure S353. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.02

Table S354. 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 S354. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00807 (Fisher's exact test), Q value = 0.014

Table S355. Gene #53: 'del_6q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 17(6Q14.1) MUTATED	18	3	4	22	4	14
DEL PEAK 17(6Q14.1) WILD-TYPE	66	54	31	54	24	47

Figure S355. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q24.3' versus 'CN_CNMF'

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

Table S356. Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 18(6Q24.3) MUTATED	26	11	11	24	6
DEL PEAK 18(6Q24.3) WILD-TYPE	97	176	25	52	13

Figure S356. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0035

Table S357. Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 18(6Q24.3) MUTATED	35	15	3	15
DEL PEAK 18(6Q24.3) WILD-TYPE	89	106	39	91

Figure S357. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.042

Table S358. Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 18(6Q24.3) MUTATED	6	4	9	6	16
DEL PEAK 18(6Q24.3) WILD-TYPE	56	58	35	34	48

Figure S358. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.046

Table S359. 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 S359. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.066

Table S360. Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 18(6Q24.3) MUTATED	17	15	8	9	4	4
DEL PEAK 18(6Q24.3) WILD-TYPE	56	42	51	51	29	55

Figure S360. 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 = 0.00335 (Fisher's exact test), Q value = 0.0065

Table S361. Gene #54: 'del_6q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 18(6Q24.3) MUTATED	17	2	2	15	5	16
DEL PEAK 18(6Q24.3) WILD-TYPE	67	55	33	61	23	45

Figure S361. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

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

Table S362. Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 19(6Q26) MUTATED	36	21	12	29	4
DEL PEAK 19(6Q26) WILD-TYPE	87	166	24	47	15

Figure S362. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.054

Table S363. Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 19(6Q26) MUTATED	40	24	6	21
DEL PEAK 19(6Q26) WILD-TYPE	84	97	36	85

Figure S363. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00088

Table S364. Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 19(6Q26) MUTATED	13	4	15	5	21
DEL PEAK 19(6Q26) WILD-TYPE	49	58	29	35	43

Figure S364. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S365. Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 19(6Q26) MUTATED	31	5	22
DEL PEAK 19(6Q26) WILD-TYPE	79	52	83

Figure S365. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00328 (Fisher's exact test), Q value = 0.0063

Table S366. 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 S366. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.032

Table S367. Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 19(6Q26) MUTATED	21	16	15	14	6	4
DEL PEAK 19(6Q26) WILD-TYPE	52	41	44	46	27	55

Figure S367. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.0017

Table S368. Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 19(6Q26) MUTATED	18	3	5	23	6	21
DEL PEAK 19(6Q26) WILD-TYPE	66	54	30	53	22	40

Figure S368. 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 = 3.8e-05

Table S369. Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 20(7Q31.1) MUTATED	33	10	1	23	4
DEL PEAK 20(7Q31.1) WILD-TYPE	90	177	35	53	15

Figure S369. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0015

Table S370. Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 20(7Q31.1) MUTATED	30	23	3	7
DEL PEAK 20(7Q31.1) WILD-TYPE	94	98	39	99

Figure S370. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.024

Table S371. Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 20(7Q31.1) MUTATED	5	7	5	6	19
DEL PEAK 20(7Q31.1) WILD-TYPE	57	55	39	34	45

Figure S371. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0012

Table S372. Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 20(7Q31.1) MUTATED	23	11	34
DEL PEAK 20(7Q31.1) WILD-TYPE	149	119	98

Figure S372. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0319 (Fisher's exact test), Q value = 0.05

Table S373. 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 S373. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

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

Table S374. Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 21(7Q36.3) MUTATED	50	8	1	31	8
DEL PEAK 21(7Q36.3) WILD-TYPE	73	179	35	45	11

Figure S374. 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 = 3.8e-05

Table S375. Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 21(7Q36.3) MUTATED	46	29	0	14
DEL PEAK 21(7Q36.3) WILD-TYPE	78	92	42	92

Figure S375. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

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

Table S376. Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 21(7Q36.3) MUTATED	7	7	7	4	28
DEL PEAK 21(7Q36.3) WILD-TYPE	55	55	37	36	36

Figure S376. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00166 (Fisher's exact test), Q value = 0.0034

Table S377. Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 21(7Q36.3) MUTATED	33	6	14
DEL PEAK 21(7Q36.3) WILD-TYPE	77	51	91

Figure S377. 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 = 3.8e-05

Table S378. Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 21(7Q36.3) MUTATED	33	13	50
DEL PEAK 21(7Q36.3) WILD-TYPE	139	117	82

Figure S378. 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 = 3.8e-05

Table S379. 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 S379. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0033

Table S380. Gene #57: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 21(7Q36.3) MUTATED	30	10	14	12	9	6
DEL PEAK 21(7Q36.3) WILD-TYPE	43	47	45	48	24	53

Figure S380. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S381. Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 21(7Q36.3) MUTATED	19	6	2	25	0	29
DEL PEAK 21(7Q36.3) WILD-TYPE	65	51	33	51	28	32

Figure S381. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

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

Table S382. Gene #58: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 22(8P23.3) MUTATED	61	16	16	33	0
DEL PEAK 22(8P23.3) WILD-TYPE	62	171	20	43	19

Figure S382. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

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

Table S383. Gene #58: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 22(8P23.3) MUTATED	61	27	3	22
DEL PEAK 22(8P23.3) WILD-TYPE	63	94	39	84

Figure S383. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'RPPA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.053

Table S384. Gene #58: 'del_8p23.3' 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 22(8P23.3) MUTATED	15	23	28	20	17
DEL PEAK 22(8P23.3) WILD-TYPE	15	69	54	73	42

Figure S384. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

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

Table S385. Gene #58: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 22(8P23.3) MUTATED	11	9	7	11	34
DEL PEAK 22(8P23.3) WILD-TYPE	51	53	37	29	30

Figure S385. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.034

Table S386. Gene #58: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 22(8P23.3) MUTATED	39	10	23
DEL PEAK 22(8P23.3) WILD-TYPE	71	47	82

Figure S386. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CNMF'

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

Table S387. Gene #58: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 22(8P23.3) MUTATED	42	24	58
DEL PEAK 22(8P23.3) WILD-TYPE	130	106	74

Figure S387. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S388. Gene #58: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 22(8P23.3) MUTATED	60	13	51
DEL PEAK 22(8P23.3) WILD-TYPE	183	69	58

Figure S388. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.061

Table S389. Gene #58: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 22(8P23.3) MUTATED	33	15	15	13	10	14
DEL PEAK 22(8P23.3) WILD-TYPE	40	42	44	47	23	45

Figure S389. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S390. Gene #58: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 22(8P23.3) MUTATED	27	5	2	28	6	32
DEL PEAK 22(8P23.3) WILD-TYPE	57	52	33	48	22	29

Figure S390. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

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

Table S391. Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 23(9P23) MUTATED	72	27	23	61	12
DEL PEAK 23(9P23) WILD-TYPE	51	160	13	15	7

Figure S391. 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 = 3.8e-05

Table S392. Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 23(9P23) MUTATED	84	46	9	37
DEL PEAK 23(9P23) WILD-TYPE	40	75	33	69

Figure S392. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00044

Table S393. 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 S393. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

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

Table S394. Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 23(9P23) MUTATED	13	19	22	14	40
DEL PEAK 23(9P23) WILD-TYPE	49	43	22	26	24

Figure S394. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S395. Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 23(9P23) MUTATED	62	49	81
DEL PEAK 23(9P23) WILD-TYPE	110	81	51

Figure S395. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S396. 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 S396. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00084

Table S397. Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 23(9P23) MUTATED	39	13	13	38	12	39
DEL PEAK 23(9P23) WILD-TYPE	45	44	22	38	16	22

Figure S397. 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 = 3.8e-05

Table S398. Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 24(9P21.3) MUTATED	73	29	21	59	11
DEL PEAK 24(9P21.3) WILD-TYPE	50	158	15	17	8

Figure S398. 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 = 3.8e-05

Table S399. Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 24(9P21.3) MUTATED	90	47	1	37
DEL PEAK 24(9P21.3) WILD-TYPE	34	74	41	69

Figure S399. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.0022

Table S400. 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 S400. 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 = 3.8e-05

Table S401. Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 24(9P21.3) MUTATED	9	19	22	16	42
DEL PEAK 24(9P21.3) WILD-TYPE	53	43	22	24	22

Figure S401. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.034

Table S402. Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 24(9P21.3) MUTATED	53	15	40
DEL PEAK 24(9P21.3) WILD-TYPE	57	42	65

Figure S402. 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 = 3.8e-05

Table S403. Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 24(9P21.3) MUTATED	59	48	83
DEL PEAK 24(9P21.3) WILD-TYPE	113	82	49

Figure S403. 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 = 3.8e-05

Table S404. 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 S404. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S405. Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 24(9P21.3) MUTATED	42	15	9	38	9	41
DEL PEAK 24(9P21.3) WILD-TYPE	42	42	26	38	19	20

Figure S405. 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 = 3.8e-05

Table S406. Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 25(9Q21.11) MUTATED	48	12	12	37	5
DEL PEAK 25(9Q21.11) WILD-TYPE	75	175	24	39	14

Figure S406. 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 = 3.8e-05

Table S407. Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 25(9Q21.11) MUTATED	53	26	2	24
DEL PEAK 25(9Q21.11) WILD-TYPE	71	95	40	82

Figure S407. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.026

Table S408. 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	7	17	19
DEL PEAK 25(9Q21.11) WILD-TYPE	94	51	61	61

Figure S408. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00982 (Fisher's exact test), Q value = 0.017

Table S409. Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 25(9Q21.11) MUTATED	8	13	12	7	25
DEL PEAK 25(9Q21.11) WILD-TYPE	54	49	32	33	39

Figure S409. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CNMF'

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

Table S410. Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 25(9Q21.11) MUTATED	30	27	55
DEL PEAK 25(9Q21.11) WILD-TYPE	142	103	77

Figure S410. 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 = 3.8e-05

Table S411. 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	47	15	50
DEL PEAK 25(9Q21.11) WILD-TYPE	196	67	59

Figure S411. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S412. Gene #61: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 25(9Q21.11) MUTATED	20	8	5	21	8	30
DEL PEAK 25(9Q21.11) WILD-TYPE	64	49	30	55	20	31

Figure S412. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p12.31' versus 'CN_CNMF'

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

Table S413. Gene #62: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 26(10P12.31) MUTATED	34	11	3	12	7
DEL PEAK 26(10P12.31) WILD-TYPE	89	176	33	64	12

Figure S413. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p12.31' versus 'METHLYATION_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.0034

Table S414. Gene #62: 'del_10p12.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 26(10P12.31) MUTATED	31	15	2	11
DEL PEAK 26(10P12.31) WILD-TYPE	93	106	40	95

Figure S414. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p12.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S415. Gene #62: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 26(10P12.31) MUTATED	20	10	36
DEL PEAK 26(10P12.31) WILD-TYPE	152	120	96

Figure S415. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p12.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0012

Table S416. Gene #62: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 26(10P12.31) MUTATED	35	4	27
DEL PEAK 26(10P12.31) WILD-TYPE	208	78	82

Figure S416. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p12.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.021 (Fisher's exact test), Q value = 0.034

Table S417. Gene #62: 'del_10p12.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 26(10P12.31) MUTATED	17	4	1	9	3	14
DEL PEAK 26(10P12.31) WILD-TYPE	67	53	34	67	25	47

Figure S417. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

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

Table S418. Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 27(10Q22.3) MUTATED	46	8	11	8	6
DEL PEAK 27(10Q22.3) WILD-TYPE	77	179	25	68	13

Figure S418. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00059

Table S419. Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 27(10Q22.3) MUTATED	38	15	3	14
DEL PEAK 27(10Q22.3) WILD-TYPE	86	106	39	92

Figure S419. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S420. Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 27(10Q22.3) MUTATED	7	3	3	9	19
DEL PEAK 27(10Q22.3) WILD-TYPE	55	59	41	31	45

Figure S420. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00039

Table S421. Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 27(10Q22.3) MUTATED	30	11	37
DEL PEAK 27(10Q22.3) WILD-TYPE	142	119	95

Figure S421. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S422. 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 S422. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.06

Table S423. Gene #63: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 27(10Q22.3) MUTATED	22	9	7	7	4	7
DEL PEAK 27(10Q22.3) WILD-TYPE	51	48	52	53	29	52

Figure S423. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S424. Gene #63: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 27(10Q22.3) MUTATED	24	3	2	8	3	16
DEL PEAK 27(10Q22.3) WILD-TYPE	60	54	33	68	25	45

Figure S424. 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 = 3.8e-05

Table S425. Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 28(10Q23.31) MUTATED	66	13	11	18	8
DEL PEAK 28(10Q23.31) WILD-TYPE	57	174	25	58	11

Figure S425. 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 = 3.8e-05

Table S426. Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 28(10Q23.31) MUTATED	57	24	4	17
DEL PEAK 28(10Q23.31) WILD-TYPE	67	97	38	89

Figure S426. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.05

Table S427. 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 S427. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00807 (Fisher's exact test), Q value = 0.014

Table S428. 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 S428. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S429. Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 28(10Q23.31) MUTATED	8	5	8	13	27
DEL PEAK 28(10Q23.31) WILD-TYPE	54	57	36	27	37

Figure S429. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.052

Table S430. Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 28(10Q23.31) MUTATED	26	6	29
DEL PEAK 28(10Q23.31) WILD-TYPE	84	51	76

Figure S430. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S431. Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 28(10Q23.31) MUTATED	46	18	50
DEL PEAK 28(10Q23.31) WILD-TYPE	126	112	82

Figure S431. 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 = 3.8e-05

Table S432. 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 S432. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.0073

Table S433. Gene #64: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 28(10Q23.31) MUTATED	32	12	11	14	9	9
DEL PEAK 28(10Q23.31) WILD-TYPE	41	45	48	46	24	50

Figure S433. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00139 (Fisher's exact test), Q value = 0.0029

Table S434. Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 28(10Q23.31) MUTATED	31	7	5	16	5	23
DEL PEAK 28(10Q23.31) WILD-TYPE	53	50	30	60	23	38

Figure S434. 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 = 3.8e-05

Table S435. Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 29(11P15.5) MUTATED	51	10	8	27	1
DEL PEAK 29(11P15.5) WILD-TYPE	72	177	28	49	18

Figure S435. 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 = 3.8e-05

Table S436. Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 29(11P15.5) MUTATED	46	22	2	13
DEL PEAK 29(11P15.5) WILD-TYPE	78	99	40	93

Figure S436. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0042

Table S437. 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 S437. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.014

Table S438. Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 29(11P15.5) MUTATED	7	6	6	7	21
DEL PEAK 29(11P15.5) WILD-TYPE	55	56	38	33	43

Figure S438. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00061

Table S439. Gene #65: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 29(11P15.5) MUTATED	29	20	45
DEL PEAK 29(11P15.5) WILD-TYPE	143	110	87

Figure S439. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0018

Table S440. 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 S440. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 0.008

Table S441. Gene #65: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 29(11P15.5) MUTATED	20	8	5	18	0	19
DEL PEAK 29(11P15.5) WILD-TYPE	64	49	30	58	28	42

Figure S441. 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 = 3.8e-05

Table S442. Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 30(11Q23.2) MUTATED	42	18	7	28	4
DEL PEAK 30(11Q23.2) WILD-TYPE	81	169	29	48	15

Figure S442. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0025

Table S443. Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 30(11Q23.2) MUTATED	42	23	3	21
DEL PEAK 30(11Q23.2) WILD-TYPE	82	98	39	85

Figure S443. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0289 (Fisher's exact test), Q value = 0.046

Table S444. 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 S444. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 0.00229 (Fisher's exact test), Q value = 0.0046

Table S445. Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 30(11Q23.2) MUTATED	5	8	16	9	17
DEL PEAK 30(11Q23.2) WILD-TYPE	57	54	28	31	47

Figure S445. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.022

Table S446. Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 30(11Q23.2) MUTATED	25	9	14	16	2	10
DEL PEAK 30(11Q23.2) WILD-TYPE	48	48	45	44	31	49

Figure S446. 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 = 0.00908 (Fisher's exact test), Q value = 0.016

Table S447. Gene #66: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 30(11Q23.2) MUTATED	22	7	5	16	3	23
DEL PEAK 30(11Q23.2) WILD-TYPE	62	50	30	60	25	38

Figure S447. 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 = 3.8e-05

Table S448. Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 31(12P13.1) MUTATED	46	6	6	12	7
DEL PEAK 31(12P13.1) WILD-TYPE	77	181	30	64	12

Figure S448. 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 = 3.8e-05

Table S449. Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 31(12P13.1) MUTATED	47	16	1	5
DEL PEAK 31(12P13.1) WILD-TYPE	77	105	41	101

Figure S449. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S450. Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 31(12P13.1) MUTATED	4	5	5	4	23
DEL PEAK 31(12P13.1) WILD-TYPE	58	57	39	36	41

Figure S450. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00641 (Fisher's exact test), Q value = 0.012

Table S451. Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 31(12P13.1) MUTATED	26	5	10
DEL PEAK 31(12P13.1) WILD-TYPE	84	52	95

Figure S451. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0032

Table S452. Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 31(12P13.1) MUTATED	26	14	36
DEL PEAK 31(12P13.1) WILD-TYPE	146	116	96

Figure S452. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0012

Table S453. 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 S453. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00862 (Fisher's exact test), Q value = 0.015

Table S454. Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 31(12P13.1) MUTATED	17	5	3	15	4	21
DEL PEAK 31(12P13.1) WILD-TYPE	67	52	32	61	24	40

Figure S454. 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 = 3.8e-05

Table S455. Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 32(12Q12) MUTATED	34	5	5	12	3
DEL PEAK 32(12Q12) WILD-TYPE	89	182	31	64	16

Figure S455. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

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

Table S456. Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 32(12Q12) MUTATED	32	12	0	10
DEL PEAK 32(12Q12) WILD-TYPE	92	109	42	96

Figure S456. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.031

Table S457. 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 S457. 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 = 3.8e-05

Table S458. Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 33(13Q12.11) MUTATED	25	9	3	23	3
DEL PEAK 33(13Q12.11) WILD-TYPE	98	178	33	53	16

Figure S458. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0466 (Fisher's exact test), Q value = 0.068

Table S459. Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 33(13Q12.11) MUTATED	25	18	2	11
DEL PEAK 33(13Q12.11) WILD-TYPE	99	103	40	95

Figure S459. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.067

Table S460. Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 33(13Q12.11) MUTATED	23	6	10
DEL PEAK 33(13Q12.11) WILD-TYPE	87	51	95

Figure S460. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.051

Table S461. Gene #69: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 33(13Q12.11) MUTATED	13	5	1	19	3	9
DEL PEAK 33(13Q12.11) WILD-TYPE	71	52	34	57	25	52

Figure S461. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

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

Table S462. Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 34(14Q23.3) MUTATED	61	19	6	43	7
DEL PEAK 34(14Q23.3) WILD-TYPE	62	168	30	33	12

Figure S462. 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 = 3.8e-05

Table S463. Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 34(14Q23.3) MUTATED	70	29	6	18
DEL PEAK 34(14Q23.3) WILD-TYPE	54	92	36	88

Figure S463. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S464. Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 34(14Q23.3) MUTATED	11	14	12	6	34
DEL PEAK 34(14Q23.3) WILD-TYPE	51	48	32	34	30

Figure S464. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0049

Table S465. Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 34(14Q23.3) MUTATED	44	11	22
DEL PEAK 34(14Q23.3) WILD-TYPE	66	46	83

Figure S465. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

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

Table S466. Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 34(14Q23.3) MUTATED	43	27	62
DEL PEAK 34(14Q23.3) WILD-TYPE	129	103	70

Figure S466. 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 = 3.8e-05

Table S467. 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 S467. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.045

Table S468. Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 34(14Q23.3) MUTATED	34	15	13	16	11	14
DEL PEAK 34(14Q23.3) WILD-TYPE	39	42	46	44	22	45

Figure S468. 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 = 0.00023 (Fisher's exact test), Q value = 0.00059

Table S469. Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 34(14Q23.3) MUTATED	21	10	6	30	5	31
DEL PEAK 34(14Q23.3) WILD-TYPE	63	47	29	46	23	30

Figure S469. 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 = 3.8e-05

Table S470. Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 35(14Q32.32) MUTATED	55	20	4	48	6
DEL PEAK 35(14Q32.32) WILD-TYPE	68	167	32	28	13

Figure S470. 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 = 3.8e-05

Table S471. Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 35(14Q32.32) MUTATED	62	28	8	21
DEL PEAK 35(14Q32.32) WILD-TYPE	62	93	34	85

Figure S471. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0024

Table S472. Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 35(14Q32.32) MUTATED	15	15	11	6	32
DEL PEAK 35(14Q32.32) WILD-TYPE	47	47	33	34	32

Figure S472. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0018

Table S473. Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 35(14Q32.32) MUTATED	46	12	21
DEL PEAK 35(14Q32.32) WILD-TYPE	64	45	84

Figure S473. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00077

Table S474. Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 35(14Q32.32) MUTATED	45	28	57
DEL PEAK 35(14Q32.32) WILD-TYPE	127	102	75

Figure S474. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.0078

Table S475. 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 S475. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0015 (Fisher's exact test), Q value = 0.0031

Table S476. Gene #71: 'del_14q32.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 35(14Q32.32) MUTATED	20	12	5	31	5	27
DEL PEAK 35(14Q32.32) WILD-TYPE	64	45	30	45	23	34

Figure S476. 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 = 3.8e-05

Table S477. Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 36(15Q11.2) MUTATED	61	16	10	27	6
DEL PEAK 36(15Q11.2) WILD-TYPE	62	171	26	49	13

Figure S477. 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 = 3.8e-05

Table S478. Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 36(15Q11.2) MUTATED	56	30	4	20
DEL PEAK 36(15Q11.2) WILD-TYPE	68	91	38	86

Figure S478. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S479. 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 S479. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0049

Table S480. 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 S480. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

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

Table S481. Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 36(15Q11.2) MUTATED	9	3	14	9	31
DEL PEAK 36(15Q11.2) WILD-TYPE	53	59	30	31	33

Figure S481. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S482. Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 36(15Q11.2) MUTATED	36	4	26
DEL PEAK 36(15Q11.2) WILD-TYPE	74	53	79

Figure S482. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

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

Table S483. Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 36(15Q11.2) MUTATED	45	22	51
DEL PEAK 36(15Q11.2) WILD-TYPE	127	108	81

Figure S483. 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 = 3.8e-05

Table S484. 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 S484. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.037

Table S485. Gene #72: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 36(15Q11.2) MUTATED	26	21	15	16	9	7
DEL PEAK 36(15Q11.2) WILD-TYPE	47	36	44	44	24	52

Figure S485. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S486. Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 36(15Q11.2) MUTATED	28	5	5	27	3	26
DEL PEAK 36(15Q11.2) WILD-TYPE	56	52	30	49	25	35

Figure S486. 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 = 3.8e-05

Table S487. Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 37(15Q15.1) MUTATED	63	15	9	29	6
DEL PEAK 37(15Q15.1) WILD-TYPE	60	172	27	47	13

Figure S487. 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 = 3.8e-05

Table S488. Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 37(15Q15.1) MUTATED	59	27	5	18
DEL PEAK 37(15Q15.1) WILD-TYPE	65	94	37	88

Figure S488. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.005

Table S489. 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 S489. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q15.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.035

Table S490. 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 S490. 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 = 3.8e-05

Table S491. Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 37(15Q15.1) MUTATED	11	3	15	8	31
DEL PEAK 37(15Q15.1) WILD-TYPE	51	59	29	32	33

Figure S491. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S492. Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 37(15Q15.1) MUTATED	41	3	24
DEL PEAK 37(15Q15.1) WILD-TYPE	69	54	81

Figure S492. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

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

Table S493. Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 37(15Q15.1) MUTATED	45	21	54
DEL PEAK 37(15Q15.1) WILD-TYPE	127	109	78

Figure S493. 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 = 3.8e-05

Table S494. 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 S494. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0071 (Fisher's exact test), Q value = 0.013

Table S495. Gene #73: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 37(15Q15.1) MUTATED	29	17	15	16	9	6
DEL PEAK 37(15Q15.1) WILD-TYPE	44	40	44	44	24	53

Figure S495. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S496. Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 37(15Q15.1) MUTATED	27	5	4	25	4	27
DEL PEAK 37(15Q15.1) WILD-TYPE	57	52	31	51	24	34

Figure S496. 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 = 3.8e-05

Table S497. Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 38(16P13.3) MUTATED	54	10	3	24	2
DEL PEAK 38(16P13.3) WILD-TYPE	69	177	33	52	17

Figure S497. 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 = 3.8e-05

Table S498. Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 38(16P13.3) MUTATED	48	20	1	15
DEL PEAK 38(16P13.3) WILD-TYPE	76	101	41	91

Figure S498. 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 = 3.8e-05

Table S499. Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 38(16P13.3) MUTATED	8	6	3	3	30
DEL PEAK 38(16P13.3) WILD-TYPE	54	56	41	37	34

Figure S499. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00046

Table S500. Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 38(16P13.3) MUTATED	33	4	13
DEL PEAK 38(16P13.3) WILD-TYPE	77	53	92

Figure S500. 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 = 3.8e-05

Table S501. Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 38(16P13.3) MUTATED	23	15	54
DEL PEAK 38(16P13.3) WILD-TYPE	149	115	78

Figure S501. 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 = 3.8e-05

Table S502. 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	36	9	47
DEL PEAK 38(16P13.3) WILD-TYPE	207	73	62

Figure S502. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S503. Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 38(16P13.3) MUTATED	33	11	4	9	11	5
DEL PEAK 38(16P13.3) WILD-TYPE	40	46	55	51	22	54

Figure S503. 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 = 3.8e-05

Table S504. Gene #74: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 38(16P13.3) MUTATED	20	5	2	15	1	30
DEL PEAK 38(16P13.3) WILD-TYPE	64	52	33	61	27	31

Figure S504. 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 = 3.8e-05

Table S505. Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 39(16Q23.1) MUTATED	74	43	13	44	8
DEL PEAK 39(16Q23.1) WILD-TYPE	49	144	23	32	11

Figure S505. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0012

Table S506. Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 39(16Q23.1) MUTATED	66	53	13	29
DEL PEAK 39(16Q23.1) WILD-TYPE	58	68	29	77

Figure S506. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.0081

Table S507. Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 39(16Q23.1) MUTATED	25	17	14	12	37
DEL PEAK 39(16Q23.1) WILD-TYPE	37	45	30	28	27

Figure S507. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00353 (Fisher's exact test), Q value = 0.0067

Table S508. Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 39(16Q23.1) MUTATED	55	14	36
DEL PEAK 39(16Q23.1) WILD-TYPE	55	43	69

Figure S508. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00013

Table S509. Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 39(16Q23.1) MUTATED	68	37	74
DEL PEAK 39(16Q23.1) WILD-TYPE	104	93	58

Figure S509. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00334 (Fisher's exact test), Q value = 0.0064

Table S510. 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 S510. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.031

Table S511. Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 39(16Q23.1) MUTATED	37	27	21	20	17	15
DEL PEAK 39(16Q23.1) WILD-TYPE	36	30	38	40	16	44

Figure S511. 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 = 3e-04 (Fisher's exact test), Q value = 0.00075

Table S512. Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 39(16Q23.1) MUTATED	37	13	9	36	7	35
DEL PEAK 39(16Q23.1) WILD-TYPE	47	44	26	40	21	26

Figure S512. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

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

Table S513. Gene #76: 'del_17p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 40(17P13.3) MUTATED	80	18	17	52	9
DEL PEAK 40(17P13.3) WILD-TYPE	43	169	19	24	10

Figure S513. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

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

Table S514. Gene #76: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 40(17P13.3) MUTATED	83	44	4	29
DEL PEAK 40(17P13.3) WILD-TYPE	41	77	38	77

Figure S514. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

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

Table S515. Gene #76: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 40(17P13.3) MUTATED	69	13	33	25
DEL PEAK 40(17P13.3) WILD-TYPE	71	45	45	55

Figure S515. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00041

Table S516. Gene #76: 'del_17p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 40(17P13.3) MUTATED	14	14	17	14	37
DEL PEAK 40(17P13.3) WILD-TYPE	48	48	27	26	27

Figure S516. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.045

Table S517. Gene #76: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 40(17P13.3) MUTATED	49	15	32
DEL PEAK 40(17P13.3) WILD-TYPE	61	42	73

Figure S517. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

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

Table S518. Gene #76: 'del_17p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 40(17P13.3) MUTATED	60	35	76
DEL PEAK 40(17P13.3) WILD-TYPE	112	95	56

Figure S518. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S519. Gene #76: 'del_17p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 40(17P13.3) MUTATED	89	19	63
DEL PEAK 40(17P13.3) WILD-TYPE	154	63	46

Figure S519. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S520. Gene #76: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 40(17P13.3) MUTATED	34	12	7	38	8	38
DEL PEAK 40(17P13.3) WILD-TYPE	50	45	28	38	20	23

Figure S520. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

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

Table S521. Gene #77: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 41(17P12) MUTATED	88	17	17	52	7
DEL PEAK 41(17P12) WILD-TYPE	35	170	19	24	12

Figure S521. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

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

Table S522. Gene #77: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 41(17P12) MUTATED	90	45	4	26
DEL PEAK 41(17P12) WILD-TYPE	34	76	38	80

Figure S522. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.028

Table S523. Gene #77: '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 41(17P12) MUTATED	17	45	29	27	25
DEL PEAK 41(17P12) WILD-TYPE	13	47	53	66	34

Figure S523. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00144 (Fisher's exact test), Q value = 0.003

Table S524. Gene #77: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	140	58	78	80
DEL PEAK 41(17P12) MUTATED	69	16	36	22
DEL PEAK 41(17P12) WILD-TYPE	71	42	42	58

Figure S524. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

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

Table S525. Gene #77: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 41(17P12) MUTATED	15	11	17	13	42
DEL PEAK 41(17P12) WILD-TYPE	47	51	27	27	22

Figure S525. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S526. Gene #77: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 41(17P12) MUTATED	52	10	36
DEL PEAK 41(17P12) WILD-TYPE	58	47	69

Figure S526. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

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

Table S527. Gene #77: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 41(17P12) MUTATED	64	29	83
DEL PEAK 41(17P12) WILD-TYPE	108	101	49

Figure S527. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S528. Gene #77: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 41(17P12) MUTATED	90	16	70
DEL PEAK 41(17P12) WILD-TYPE	153	66	39

Figure S528. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00621 (Fisher's exact test), Q value = 0.011

Table S529. Gene #77: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 41(17P12) MUTATED	43	23	22	25	12	15
DEL PEAK 41(17P12) WILD-TYPE	30	34	37	35	21	44

Figure S529. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S530. Gene #77: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 41(17P12) MUTATED	39	9	7	39	6	40
DEL PEAK 41(17P12) WILD-TYPE	45	48	28	37	22	21

Figure S530. Get High-res Image Gene #77: '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 = 3.8e-05

Table S531. Gene #78: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 42(17Q24.3) MUTATED	35	10	6	19	6
DEL PEAK 42(17Q24.3) WILD-TYPE	88	177	30	57	13

Figure S531. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00016

Table S532. Gene #78: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 42(17Q24.3) MUTATED	32	20	0	12
DEL PEAK 42(17Q24.3) WILD-TYPE	92	101	42	94

Figure S532. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.033

Table S533. Gene #78: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 42(17Q24.3) MUTATED	7	6	4	10	17
DEL PEAK 42(17Q24.3) WILD-TYPE	55	56	40	30	47

Figure S533. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.011

Table S534. Gene #78: 'del_17q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 42(17Q24.3) MUTATED	25	15	34
DEL PEAK 42(17Q24.3) WILD-TYPE	147	115	98

Figure S534. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.023

Table S535. Gene #78: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 42(17Q24.3) MUTATED	34	11	29
DEL PEAK 42(17Q24.3) WILD-TYPE	209	71	80

Figure S535. Get High-res Image Gene #78: '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 = 3.8e-05

Table S536. Gene #79: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 43(18Q12.2) MUTATED	82	29	20	46	4
DEL PEAK 43(18Q12.2) WILD-TYPE	41	158	16	30	15

Figure S536. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

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

Table S537. Gene #79: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 43(18Q12.2) MUTATED	71	39	20	29
DEL PEAK 43(18Q12.2) WILD-TYPE	53	82	22	77

Figure S537. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.031

Table S538. Gene #79: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 43(18Q12.2) MUTATED	21	19	20	10	34
DEL PEAK 43(18Q12.2) WILD-TYPE	41	43	24	30	30

Figure S538. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0041

Table S539. Gene #79: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 43(18Q12.2) MUTATED	56	16	32
DEL PEAK 43(18Q12.2) WILD-TYPE	54	41	73

Figure S539. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S540. Gene #79: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 43(18Q12.2) MUTATED	62	42	74
DEL PEAK 43(18Q12.2) WILD-TYPE	110	88	58

Figure S540. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00073

Table S541. Gene #79: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 43(18Q12.2) MUTATED	91	25	62
DEL PEAK 43(18Q12.2) WILD-TYPE	152	57	47

Figure S541. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.0084

Table S542. Gene #79: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 43(18Q12.2) MUTATED	41	17	19	27	15	16
DEL PEAK 43(18Q12.2) WILD-TYPE	32	40	40	33	18	43

Figure S542. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00075

Table S543. Gene #79: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 43(18Q12.2) MUTATED	34	12	9	31	11	38
DEL PEAK 43(18Q12.2) WILD-TYPE	50	45	26	45	17	23

Figure S543. Get High-res Image Gene #79: '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 = 3.8e-05

Table S544. Gene #80: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 44(18Q21.2) MUTATED	89	35	25	51	4
DEL PEAK 44(18Q21.2) WILD-TYPE	34	152	11	25	15

Figure S544. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S545. Gene #80: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 44(18Q21.2) MUTATED	79	49	21	33
DEL PEAK 44(18Q21.2) WILD-TYPE	45	72	21	73

Figure S545. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0018

Table S546. Gene #80: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 44(18Q21.2) MUTATED	26	20	20	12	42
DEL PEAK 44(18Q21.2) WILD-TYPE	36	42	24	28	22

Figure S546. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0012

Table S547. Gene #80: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 44(18Q21.2) MUTATED	64	17	39
DEL PEAK 44(18Q21.2) WILD-TYPE	46	40	66

Figure S547. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00053

Table S548. Gene #80: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 44(18Q21.2) MUTATED	74	47	80
DEL PEAK 44(18Q21.2) WILD-TYPE	98	83	52

Figure S548. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S549. Gene #80: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 44(18Q21.2) MUTATED	106	28	67
DEL PEAK 44(18Q21.2) WILD-TYPE	137	54	42

Figure S549. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.012

Table S550. Gene #80: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 44(18Q21.2) MUTATED	45	19	23	31	15	20
DEL PEAK 44(18Q21.2) WILD-TYPE	28	38	36	29	18	39

Figure S550. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.0026

Table S551. Gene #80: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 44(18Q21.2) MUTATED	43	14	11	35	13	37
DEL PEAK 44(18Q21.2) WILD-TYPE	41	43	24	41	15	24

Figure S551. Get High-res Image Gene #80: '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 = 3.8e-05

Table S552. Gene #81: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 45(19P13.3) MUTATED	92	9	12	42	7
DEL PEAK 45(19P13.3) WILD-TYPE	31	178	24	34	12

Figure S552. Get High-res Image Gene #81: '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 = 3.8e-05

Table S553. Gene #81: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 45(19P13.3) MUTATED	92	30	5	19
DEL PEAK 45(19P13.3) WILD-TYPE	32	91	37	87

Figure S553. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S554. Gene #81: '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 45(19P13.3) MUTATED	73	14	26	21
DEL PEAK 45(19P13.3) WILD-TYPE	67	44	52	59

Figure S554. Get High-res Image Gene #81: '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 = 3.8e-05

Table S555. Gene #81: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 45(19P13.3) MUTATED	13	4	11	9	48
DEL PEAK 45(19P13.3) WILD-TYPE	49	58	33	31	16

Figure S555. Get High-res Image Gene #81: '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 = 3.8e-05

Table S556. Gene #81: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 45(19P13.3) MUTATED	54	5	26
DEL PEAK 45(19P13.3) WILD-TYPE	56	52	79

Figure S556. Get High-res Image Gene #81: '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 = 3.8e-05

Table S557. Gene #81: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 45(19P13.3) MUTATED	46	23	90
DEL PEAK 45(19P13.3) WILD-TYPE	126	107	42

Figure S557. Get High-res Image Gene #81: '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 = 3.8e-05

Table S558. Gene #81: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 45(19P13.3) MUTATED	66	8	85
DEL PEAK 45(19P13.3) WILD-TYPE	177	74	24

Figure S558. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S559. Gene #81: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 45(19P13.3) MUTATED	47	16	18	23	16	7
DEL PEAK 45(19P13.3) WILD-TYPE	26	41	41	37	17	52

Figure S559. Get High-res Image Gene #81: '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 = 3.8e-05

Table S560. Gene #81: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 45(19P13.3) MUTATED	37	6	3	29	2	50
DEL PEAK 45(19P13.3) WILD-TYPE	47	51	32	47	26	11

Figure S560. Get High-res Image Gene #81: '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 = 3.8e-05

Table S561. Gene #82: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 46(19Q13.11) MUTATED	41	5	6	16	7
DEL PEAK 46(19Q13.11) WILD-TYPE	82	182	30	60	12

Figure S561. Get High-res Image Gene #82: '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 = 3.8e-05

Table S562. Gene #82: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 46(19Q13.11) MUTATED	47	16	1	4
DEL PEAK 46(19Q13.11) WILD-TYPE	77	105	41	102

Figure S562. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00075

Table S563. Gene #82: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 46(19Q13.11) MUTATED	6	2	6	4	20
DEL PEAK 46(19Q13.11) WILD-TYPE	56	60	38	36	44

Figure S563. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00919 (Fisher's exact test), Q value = 0.016

Table S564. Gene #82: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	110	57	105
DEL PEAK 46(19Q13.11) MUTATED	22	2	14
DEL PEAK 46(19Q13.11) WILD-TYPE	88	55	91

Figure S564. Get High-res Image Gene #82: '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 = 3.8e-05

Table S565. Gene #82: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 46(19Q13.11) MUTATED	23	8	43
DEL PEAK 46(19Q13.11) WILD-TYPE	149	122	89

Figure S565. Get High-res Image Gene #82: '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 = 3.8e-05

Table S566. Gene #82: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 46(19Q13.11) MUTATED	28	4	42
DEL PEAK 46(19Q13.11) WILD-TYPE	215	78	67

Figure S566. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0045

Table S567. Gene #82: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 46(19Q13.11) MUTATED	24	11	9	6	6	4
DEL PEAK 46(19Q13.11) WILD-TYPE	49	46	50	54	27	55

Figure S567. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S568. Gene #82: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 46(19Q13.11) MUTATED	22	2	2	11	0	23
DEL PEAK 46(19Q13.11) WILD-TYPE	62	55	33	65	28	38

Figure S568. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

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

Table S569. Gene #83: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 47(20P12.1) MUTATED	20	8	1	10	0
DEL PEAK 47(20P12.1) WILD-TYPE	103	179	35	66	19

Figure S569. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S570. Gene #83: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 47(20P12.1) MUTATED	24	7	1	5
DEL PEAK 47(20P12.1) WILD-TYPE	100	114	41	101

Figure S570. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.034

Table S571. Gene #83: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 47(20P12.1) MUTATED	3	2	8	1	8
DEL PEAK 47(20P12.1) WILD-TYPE	59	60	36	39	56

Figure S571. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S572. Gene #83: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 47(20P12.1) MUTATED	10	6	23
DEL PEAK 47(20P12.1) WILD-TYPE	162	124	109

Figure S572. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.046

Table S573. Gene #83: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 47(20P12.1) MUTATED	20	3	16
DEL PEAK 47(20P12.1) WILD-TYPE	223	79	93

Figure S573. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

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

Table S574. Gene #84: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 48(21Q11.2) MUTATED	75	35	16	46	11
DEL PEAK 48(21Q11.2) WILD-TYPE	48	152	20	30	8

Figure S574. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S575. Gene #84: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 48(21Q11.2) MUTATED	74	48	7	39
DEL PEAK 48(21Q11.2) WILD-TYPE	50	73	35	67

Figure S575. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0017

Table S576. Gene #84: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 48(21Q11.2) MUTATED	18	17	11	11	37
DEL PEAK 48(21Q11.2) WILD-TYPE	44	45	33	29	27

Figure S576. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

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

Table S577. Gene #84: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 48(21Q11.2) MUTATED	60	40	80
DEL PEAK 48(21Q11.2) WILD-TYPE	112	90	52

Figure S577. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0014

Table S578. Gene #84: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 48(21Q11.2) MUTATED	92	26	62
DEL PEAK 48(21Q11.2) WILD-TYPE	151	56	47

Figure S578. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00503 (Fisher's exact test), Q value = 0.0093

Table S579. Gene #84: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 48(21Q11.2) MUTATED	38	25	18	27	21	17
DEL PEAK 48(21Q11.2) WILD-TYPE	35	32	41	33	12	42

Figure S579. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S580. Gene #84: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 48(21Q11.2) MUTATED	35	16	8	41	9	37
DEL PEAK 48(21Q11.2) WILD-TYPE	49	41	27	35	19	24

Figure S580. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.3' versus 'CN_CNMF'

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

Table S581. Gene #85: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 49(21Q22.3) MUTATED	73	39	17	53	11
DEL PEAK 49(21Q22.3) WILD-TYPE	50	148	19	23	8

Figure S581. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 9.9e-05

Table S582. Gene #85: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 49(21Q22.3) MUTATED	71	55	6	42
DEL PEAK 49(21Q22.3) WILD-TYPE	53	66	36	64

Figure S582. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 0.035 (Fisher's exact test), Q value = 0.054

Table S583. Gene #85: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 49(21Q22.3) MUTATED	19	18	16	12	34
DEL PEAK 49(21Q22.3) WILD-TYPE	43	44	28	28	30

Figure S583. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00018

Table S584. Gene #85: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 49(21Q22.3) MUTATED	71	42	77
DEL PEAK 49(21Q22.3) WILD-TYPE	101	88	55

Figure S584. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00082

Table S585. Gene #85: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 49(21Q22.3) MUTATED	103	24	63
DEL PEAK 49(21Q22.3) WILD-TYPE	140	58	46

Figure S585. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0014

Table S586. Gene #85: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 49(21Q22.3) MUTATED	38	31	22	24	23	16
DEL PEAK 49(21Q22.3) WILD-TYPE	35	26	37	36	10	43

Figure S586. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00049

Table S587. Gene #85: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 49(21Q22.3) MUTATED	42	16	9	45	8	34
DEL PEAK 49(21Q22.3) WILD-TYPE	42	41	26	31	20	27

Figure S587. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

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

Table S588. Gene #86: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 50(22Q13.31) MUTATED	73	21	11	47	9
DEL PEAK 50(22Q13.31) WILD-TYPE	50	166	25	29	10

Figure S588. Get High-res Image Gene #86: '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 = 3.8e-05

Table S589. Gene #86: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 50(22Q13.31) MUTATED	75	40	4	25
DEL PEAK 50(22Q13.31) WILD-TYPE	49	81	38	81

Figure S589. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.016

Table S590. Gene #86: '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 50(22Q13.31) MUTATED	62	13	29	22
DEL PEAK 50(22Q13.31) WILD-TYPE	78	45	49	58

Figure S590. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0013

Table S591. Gene #86: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 50(22Q13.31) MUTATED	14	14	17	11	35
DEL PEAK 50(22Q13.31) WILD-TYPE	48	48	27	29	29

Figure S591. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CNMF'

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

Table S592. Gene #86: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 50(22Q13.31) MUTATED	51	31	76
DEL PEAK 50(22Q13.31) WILD-TYPE	121	99	56

Figure S592. Get High-res Image Gene #86: '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 = 3.8e-05

Table S593. Gene #86: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 50(22Q13.31) MUTATED	77	17	64
DEL PEAK 50(22Q13.31) WILD-TYPE	166	65	45

Figure S593. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00059

Table S594. Gene #86: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 50(22Q13.31) MUTATED	39	23	21	14	18	13
DEL PEAK 50(22Q13.31) WILD-TYPE	34	34	38	46	15	46

Figure S594. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00021

Table S595. Gene #86: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 50(22Q13.31) MUTATED	34	13	6	34	6	35
DEL PEAK 50(22Q13.31) WILD-TYPE	50	44	29	42	22	26

Figure S595. Get High-res Image Gene #86: '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 = 3.8e-05

Table S596. Gene #87: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 51(XP22.2) MUTATED	42	11	4	24	4
DEL PEAK 51(XP22.2) WILD-TYPE	81	176	32	52	15

Figure S596. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00053

Table S597. Gene #87: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 51(XP22.2) MUTATED	39	24	2	14
DEL PEAK 51(XP22.2) WILD-TYPE	85	97	40	92

Figure S597. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00054

Table S598. Gene #87: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 51(XP22.2) MUTATED	3	7	9	11	21
DEL PEAK 51(XP22.2) WILD-TYPE	59	55	35	29	43

Figure S598. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0036

Table S599. Gene #87: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 51(XP22.2) MUTATED	40	10	34
DEL PEAK 51(XP22.2) WILD-TYPE	203	72	75

Figure S599. Get High-res Image Gene #87: '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 = 3.8e-05

Table S600. Gene #88: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 52(XP21.1) MUTATED	35	8	7	21	3
DEL PEAK 52(XP21.1) WILD-TYPE	88	179	29	55	16

Figure S600. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00358 (Fisher's exact test), Q value = 0.0068

Table S601. Gene #88: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 52(XP21.1) MUTATED	29	23	1	13
DEL PEAK 52(XP21.1) WILD-TYPE	95	98	41	93

Figure S601. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.033

Table S602. Gene #88: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 52(XP21.1) MUTATED	2	9	8	7	14
DEL PEAK 52(XP21.1) WILD-TYPE	60	53	36	33	50

Figure S602. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'CN_CNMF'

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

Table S603. Gene #89: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 53(XQ21.33) MUTATED	27	6	5	17	1
DEL PEAK 53(XQ21.33) WILD-TYPE	96	181	31	59	18

Figure S603. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.0073

Table S604. Gene #89: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 53(XQ21.33) MUTATED	25	15	2	6
DEL PEAK 53(XQ21.33) WILD-TYPE	99	106	40	100

Figure S604. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.0252 (Fisher's exact test), Q value = 0.04

Table S605. Gene #89: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	62	62	44	40	64
DEL PEAK 53(XQ21.33) MUTATED	3	5	6	5	15
DEL PEAK 53(XQ21.33) WILD-TYPE	59	57	38	35	49

Figure S605. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.057

Table S606. Gene #89: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	130	132
DEL PEAK 53(XQ21.33) MUTATED	21	10	24
DEL PEAK 53(XQ21.33) WILD-TYPE	151	120	108

Figure S606. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.041

Table S607. Gene #89: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	243	82	109
DEL PEAK 53(XQ21.33) MUTATED	32	4	19
DEL PEAK 53(XQ21.33) WILD-TYPE	211	78	90

Figure S607. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.071

Table S608. Gene #89: 'del_xq21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	73	57	59	60	33	59
DEL PEAK 53(XQ21.33) MUTATED	17	5	4	8	4	4
DEL PEAK 53(XQ21.33) WILD-TYPE	56	52	55	52	29	55

Figure S608. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xq21.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.058

Table S609. Gene #89: 'del_xq21.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	84	57	35	76	28	61
DEL PEAK 53(XQ21.33) MUTATED	15	3	1	9	2	12
DEL PEAK 53(XQ21.33) WILD-TYPE	69	54	34	67	26	49

Figure S609. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/19782340/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/20140953/STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly focal cnvs = 89
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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