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 94 focal events and 10 molecular subtypes across 625 patients, 683 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p34.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 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_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_2q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 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_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', 'RPPA_CHIERARCHICAL', '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_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.
amp_9p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_10q26.13 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 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_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_1q44 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q22.1 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_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q33.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 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_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', '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_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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', and 'MIRSEQ_MATURE_CNMF'.
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_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', '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_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 94 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, 683 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 6p21 1	192 (31%)	433	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0236 (0.0348)	0.0119 (0.0185)	4e-05 (9.89e-05)	1e-05 (2.81e-05)	0.00018 (0.000394)	1e-05 (2.81e-05)	2e-05 (5.28e-05)	1e-05 (2.81e-05)
del 1p36 11	210 (34%)	415	1e-05 (2.81e-05)	3e-05 (7.62e-05)	0.00534 (0.0089)	0.00267 (0.0047)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00021 (0.000451)	1e-05 (2.81e-05)	0.00187 (0.00339)	3e-05 (7.62e-05)
del 5q12 1	282 (45%)	343	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00196 (0.00354)	0.00289 (0.00507)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 11p15 5	175 (28%)	450	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0135 (0.0208)	0.00522 (0.00872)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	3e-05 (7.62e-05)	1e-05 (2.81e-05)	0.00124 (0.00231)	0.00044 (0.000893)
del 19p13 3	249 (40%)	376	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00359 (0.00615)	0.00083 (0.00161)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
amp 1q21 3	249 (40%)	376	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.887 (0.906)	0.0139 (0.0212)	0.00124 (0.00231)	1e-05 (2.81e-05)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
amp 1q42 3	244 (39%)	381	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.706 (0.741)	0.0456 (0.063)	0.00057 (0.00114)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
amp 5p15 33	228 (36%)	397	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.187 (0.229)	0.00604 (0.00993)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
amp 11q13 3	218 (35%)	407	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0505 (0.0693)	0.0419 (0.0583)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
amp 15q26 1	168 (27%)	457	1e-05 (2.81e-05)	0.00347 (0.00596)	0.00212 (0.00381)	0.00651 (0.0107)	3e-05 (7.62e-05)	1e-05 (2.81e-05)	0.0111 (0.0175)	0.00011 (0.000253)	0.051 (0.0699)	0.00039 (8e-04)
del 2q22 1	126 (20%)	499	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.428 (0.477)	0.0236 (0.0348)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 3p14 2	282 (45%)	343	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.46 (0.509)	0.0379 (0.0531)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 8p23 2	214 (34%)	411	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.82 (0.85)	0.0167 (0.0253)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	7e-05 (0.000164)	1e-05 (2.81e-05)
del 10q23 31	183 (29%)	442	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00765 (0.0123)	0.0548 (0.0745)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00012 (0.000272)	1e-05 (2.81e-05)	0.00173 (0.00316)	1e-05 (2.81e-05)
del 15q11 2	183 (29%)	442	1e-05 (2.81e-05)	0.00722 (0.0117)	0.0299 (0.0428)	0.0309 (0.044)	0.00276 (0.00485)	2e-05 (5.28e-05)	0.027 (0.0391)	1e-05 (2.81e-05)	0.0412 (0.0574)	0.428 (0.477)
amp 2q12 2	155 (25%)	470	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.461 (0.509)	0.68 (0.716)	4e-05 (9.89e-05)	1e-05 (2.81e-05)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	0.00018 (0.000394)	0.00014 (0.000313)
amp 3q26 2	287 (46%)	338	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.495 (0.541)	0.953 (0.965)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
amp 5p13 1	216 (35%)	409	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.943 (0.957)	0.103 (0.135)	4e-05 (9.89e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00011 (0.000253)	1e-05 (2.81e-05)
amp 6q12	141 (23%)	484	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.469 (0.518)	0.234 (0.277)	0.0179 (0.027)	1e-05 (2.81e-05)	0.0294 (0.0423)	1e-05 (2.81e-05)	0.00021 (0.000451)	5e-05 (0.000121)
amp 7p22 3	353 (56%)	272	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.999 (1.00)	0.168 (0.209)	2e-05 (5.28e-05)	2e-05 (5.28e-05)	3e-05 (7.62e-05)	1e-05 (2.81e-05)	0.00033 (0.000685)	5e-05 (0.000121)
amp 7p11 2	339 (54%)	286	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.797 (0.829)	0.162 (0.202)	0.00014 (0.000313)	0.00012 (0.000272)	0.00015 (0.000333)	2e-05 (5.28e-05)	0.00021 (0.000451)	6e-05 (0.000143)
amp 7q21 2	317 (51%)	308	1e-05 (2.81e-05)	2e-05 (5.28e-05)	0.243 (0.286)	0.174 (0.216)	0.00357 (0.00612)	0.0163 (0.0246)	0.0126 (0.0195)	0.0014 (0.0026)	0.0072 (0.0117)	0.00634 (0.0104)
amp 8p23 1	229 (37%)	396	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.843 (0.868)	0.688 (0.722)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	9e-05 (0.000209)	0.0011 (0.00209)	0.00125 (0.00233)	0.00012 (0.000272)
amp 8q24 21	454 (73%)	171	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.332 (0.38)	0.15 (0.189)	0.00122 (0.00229)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	3e-05 (7.62e-05)	0.00022 (0.000469)
amp 12p12 1	207 (33%)	418	1e-05 (2.81e-05)	5e-05 (0.000121)	0.528 (0.574)	0.0867 (0.115)	0.0018 (0.00327)	2e-05 (5.28e-05)	0.00022 (0.000469)	0.00202 (0.00364)	0.00067 (0.00132)	0.00253 (0.00448)
amp 13q12 3	216 (35%)	409	1e-05 (2.81e-05)	0.0275 (0.0396)	0.0516 (0.0704)	0.826 (0.854)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0254 (0.0371)	1e-05 (2.81e-05)	0.0127 (0.0196)	1e-05 (2.81e-05)
amp 13q22 1	243 (39%)	382	1e-05 (2.81e-05)	0.0003 (0.000629)	0.412 (0.462)	0.262 (0.306)	0.00116 (0.00219)	1e-05 (2.81e-05)	0.0293 (0.0422)	1e-05 (2.81e-05)	0.00486 (0.00816)	1e-05 (2.81e-05)
amp 14q13 3	113 (18%)	512	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.558 (0.602)	0.125 (0.16)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	7e-05 (0.000164)	1e-05 (2.81e-05)
amp 18p11 32	178 (28%)	447	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.744 (0.777)	0.0552 (0.0749)	0.00161 (0.00296)	1e-05 (2.81e-05)	0.00025 (0.000528)	1e-05 (2.81e-05)	0.00084 (0.00163)	0.00038 (0.000782)
amp 19q12	185 (30%)	440	1e-05 (2.81e-05)	2e-05 (5.28e-05)	0.00041 (0.000836)	0.00087 (0.00168)	0.0625 (0.0844)	1e-05 (2.81e-05)	0.0218 (0.0324)	1e-05 (2.81e-05)	0.35 (0.397)	1e-05 (2.81e-05)
amp xq28	155 (25%)	470	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.841 (0.867)	0.249 (0.293)	1e-05 (2.81e-05)	2e-05 (5.28e-05)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	4e-05 (9.89e-05)	1e-05 (2.81e-05)
del 1p13 2	156 (25%)	469	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.123 (0.158)	0.135 (0.172)	6e-05 (0.000143)	2e-05 (5.28e-05)	0.00341 (0.00587)	2e-05 (5.28e-05)	0.0155 (0.0237)	0.0202 (0.0302)
del 2q37 2	122 (20%)	503	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.562 (0.605)	0.287 (0.332)	0.00068 (0.00134)	1e-05 (2.81e-05)	0.00139 (0.00258)	1e-05 (2.81e-05)	0.0262 (0.038)	0.00016 (0.000354)
del 3p26 2	250 (40%)	375	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.912 (0.929)	0.211 (0.253)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 4p16 3	271 (43%)	354	1e-05 (2.81e-05)	4e-05 (9.89e-05)	0.519 (0.566)	0.9 (0.917)	0.0323 (0.0457)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 4p15 2	269 (43%)	356	1e-05 (2.81e-05)	3e-05 (7.62e-05)	0.654 (0.693)	0.959 (0.968)	0.00571 (0.00947)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 4q22 1	298 (48%)	327	1e-05 (2.81e-05)	0.00024 (0.000508)	0.448 (0.498)	0.063 (0.085)	0.00092 (0.00176)	1e-05 (2.81e-05)	0.00733 (0.0119)	1e-05 (2.81e-05)	0.0182 (0.0274)	0.00515 (0.00861)
del 4q34 3	300 (48%)	325	1e-05 (2.81e-05)	0.00601 (0.00989)	0.207 (0.25)	0.338 (0.384)	0.0213 (0.0317)	1e-05 (2.81e-05)	0.024 (0.0354)	1e-05 (2.81e-05)	0.0101 (0.016)	2e-05 (5.28e-05)
del 6p25 3	188 (30%)	437	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.412 (0.462)	0.108 (0.14)	0.00036 (0.000744)	1e-05 (2.81e-05)	0.00313 (0.00542)	1e-05 (2.81e-05)	0.0408 (0.0569)	0.00059 (0.00117)
del 7q31 1	127 (20%)	498	1e-05 (2.81e-05)	4e-05 (9.89e-05)	0.541 (0.586)	0.575 (0.618)	0.00215 (0.00386)	0.00033 (0.000685)	0.0105 (0.0165)	0.00091 (0.00175)	0.0123 (0.0191)	0.00159 (0.00293)
del 7q36 3	165 (26%)	460	1e-05 (2.81e-05)	5e-05 (0.000121)	0.394 (0.444)	0.286 (0.331)	0.00041 (0.000836)	1e-05 (2.81e-05)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	0.00053 (0.00107)	0.00252 (0.00447)
del 9p23	302 (48%)	323	1e-05 (2.81e-05)	0.00296 (0.00517)	0.204 (0.247)	0.508 (0.555)	0.00082 (0.0016)	1e-05 (2.81e-05)	0.00379 (0.00645)	1e-05 (2.81e-05)	0.0302 (0.0431)	0.0299 (0.0428)
del 9p21 3	334 (53%)	291	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.198 (0.241)	0.493 (0.541)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 9q21 11	175 (28%)	450	1e-05 (2.81e-05)	0.0001 (0.000232)	0.225 (0.268)	0.343 (0.39)	0.00433 (0.00731)	1e-05 (2.81e-05)	0.00014 (0.000313)	1e-05 (2.81e-05)	0.00042 (0.000855)	0.0004 (0.000819)
del 10p15 3	131 (21%)	494	1e-05 (2.81e-05)	9e-05 (0.000209)	0.848 (0.871)	0.806 (0.837)	0.00406 (0.00688)	2e-05 (5.28e-05)	0.017 (0.0256)	1e-05 (2.81e-05)	0.00176 (0.00321)	5e-05 (0.000121)
del 10p11 21	102 (16%)	523	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.735 (0.769)	0.929 (0.944)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	8e-05 (0.000188)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 10q22 3	135 (22%)	490	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.228 (0.271)	0.184 (0.226)	7e-05 (0.000164)	1e-05 (2.81e-05)	0.00023 (0.000489)	1e-05 (2.81e-05)	0.00111 (0.0021)	1e-05 (2.81e-05)
del 11q25	178 (28%)	447	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.154 (0.194)	0.225 (0.269)	3e-05 (7.62e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	3e-05 (7.62e-05)	1e-05 (2.81e-05)
del 13q12 11	138 (22%)	487	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.44 (0.489)	0.122 (0.157)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	9e-05 (0.000209)	1e-05 (2.81e-05)
del 13q21 31	126 (20%)	499	1e-05 (2.81e-05)	4e-05 (9.89e-05)	0.257 (0.301)	0.135 (0.172)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00019 (0.000414)	1e-05 (2.81e-05)	0.00058 (0.00116)	1e-05 (2.81e-05)
del 16p13 3	177 (28%)	448	1e-05 (2.81e-05)	0.0006 (0.00119)	0.204 (0.247)	0.161 (0.201)	9e-05 (0.000209)	1e-05 (2.81e-05)	0.00055 (0.0011)	1e-05 (2.81e-05)	4e-05 (9.89e-05)	1e-05 (2.81e-05)
del 16p13 3	153 (24%)	472	1e-05 (2.81e-05)	0.00107 (0.00204)	0.192 (0.235)	0.476 (0.524)	0.00262 (0.00463)	1e-05 (2.81e-05)	0.00021 (0.000451)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)
del 16q23 1	265 (42%)	360	1e-05 (2.81e-05)	0.00065 (0.00128)	0.977 (0.984)	0.146 (0.184)	0.0393 (0.0551)	1e-05 (2.81e-05)	0.0112 (0.0176)	1e-05 (2.81e-05)	0.00313 (0.00542)	1e-05 (2.81e-05)
del 17p12	267 (43%)	358	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.197 (0.24)	0.149 (0.187)	0.00012 (0.000272)	1e-05 (2.81e-05)	5e-05 (0.000121)	1e-05 (2.81e-05)	0.0182 (0.0274)	1e-05 (2.81e-05)
del 18q21 2	323 (52%)	302	1e-05 (2.81e-05)	0.00014 (0.000313)	0.969 (0.976)	0.183 (0.225)	0.00117 (0.0022)	0.00054 (0.00109)	0.0494 (0.068)	5e-05 (0.000121)	0.00843 (0.0134)	0.00914 (0.0145)
del 21q11 2	286 (46%)	339	1e-05 (2.81e-05)	0.00302 (0.00526)	0.915 (0.931)	0.751 (0.782)	0.00022 (0.000469)	1e-05 (2.81e-05)	0.0302 (0.0431)	1e-05 (2.81e-05)	0.00368 (0.00628)	0.00671 (0.011)
del 21q22 13	305 (49%)	320	1e-05 (2.81e-05)	0.00551 (0.00917)	0.962 (0.97)	0.992 (0.995)	0.00015 (0.000333)	1e-05 (2.81e-05)	0.00769 (0.0123)	1e-05 (2.81e-05)	0.00018 (0.000394)	0.015 (0.0229)
del 22q11 1	230 (37%)	395	1e-05 (2.81e-05)	0.00323 (0.00557)	0.101 (0.132)	0.157 (0.197)	0.00307 (0.00533)	1e-05 (2.81e-05)	0.00477 (0.00802)	1e-05 (2.81e-05)	0.00363 (0.0062)	4e-05 (9.89e-05)
del 22q13 31	235 (38%)	390	1e-05 (2.81e-05)	0.00072 (0.00141)	0.682 (0.718)	0.239 (0.282)	0.00708 (0.0115)	1e-05 (2.81e-05)	0.00046 (0.000932)	1e-05 (2.81e-05)	0.00233 (0.00416)	1e-05 (2.81e-05)
del xp22 2	151 (24%)	474	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.361 (0.409)	0.109 (0.141)	3e-05 (7.62e-05)	0.0006 (0.00119)	6e-05 (0.000143)	1e-05 (2.81e-05)	0.0447 (0.0618)	0.00037 (0.000763)
del xp21 1	146 (23%)	479	1e-05 (2.81e-05)	2e-05 (5.28e-05)	0.559 (0.603)	0.177 (0.219)	1e-05 (2.81e-05)	2e-05 (5.28e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0006 (0.00119)	3e-05 (7.62e-05)
del xp11 3	148 (24%)	477	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.861 (0.883)	0.245 (0.288)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.00091 (0.00175)	1e-05 (2.81e-05)
amp 1p36 22	101 (16%)	524	1e-05 (2.81e-05)	0.00247 (0.0044)	0.46 (0.509)	0.386 (0.435)	0.326 (0.374)	1e-05 (2.81e-05)	0.0436 (0.0604)	0.00015 (0.000333)	0.0296 (0.0425)	0.0246 (0.0361)
amp 10p11 22	169 (27%)	456	1e-05 (2.81e-05)	0.00021 (0.000451)	0.998 (1)	0.674 (0.711)	0.0261 (0.038)	0.00179 (0.00326)	0.663 (0.7)	1e-05 (2.81e-05)	0.00394 (0.00669)	0.0122 (0.019)
amp 17q12	222 (36%)	403	1e-05 (2.81e-05)	0.00014 (0.000313)	0.0548 (0.0745)	0.138 (0.175)	1e-05 (2.81e-05)	1e-05 (2.81e-05)	0.0109 (0.0171)	4e-05 (9.89e-05)	0.0639 (0.0859)	0.00416 (0.00703)
amp 18q11 2	198 (32%)	427	1e-05 (2.81e-05)	0.286 (0.332)	0.877 (0.898)	0.268 (0.312)	0.00513 (0.0086)	1e-05 (2.81e-05)	0.0326 (0.0461)	0.00021 (0.000451)	0.00576 (0.00953)	0.00746 (0.012)
amp 19q13 43	164 (26%)	461	1e-05 (2.81e-05)	0.0101 (0.016)	0.0129 (0.0198)	0.0998 (0.131)	0.169 (0.21)	0.183 (0.225)	0.0215 (0.032)	6e-05 (0.000143)	0.00882 (0.014)	0.00744 (0.012)
del 2q33 3	85 (14%)	540	1e-05 (2.81e-05)	0.00012 (0.000272)	0.823 (0.852)	0.12 (0.154)	0.00158 (0.00292)	0.00266 (0.00469)	0.00012 (0.000272)	0.00011 (0.000253)	0.208 (0.251)	0.00294 (0.00515)
del 18q12 2	292 (47%)	333	1e-05 (2.81e-05)	0.00106 (0.00203)	0.956 (0.966)	0.178 (0.22)	0.00438 (0.00738)	5e-05 (0.000121)	0.137 (0.173)	0.00024 (0.000508)	0.00773 (0.0124)	0.00577 (0.00953)
del xq11 2	105 (17%)	520	1e-05 (2.81e-05)	0.00019 (0.000414)	0.127 (0.163)	0.275 (0.32)	0.00021 (0.000451)	0.0103 (0.0163)	0.00166 (0.00305)	0.00298 (0.0052)	0.0531 (0.0723)	0.0332 (0.0469)
amp 1p34 2	95 (15%)	530	1e-05 (2.81e-05)	0.00172 (0.00315)	0.641 (0.681)	0.984 (0.988)	0.229 (0.272)	3e-05 (7.62e-05)	0.116 (0.15)	0.0158 (0.024)	0.00108 (0.00206)	0.00057 (0.00114)
amp 9q34 3	185 (30%)	440	1e-05 (2.81e-05)	0.00761 (0.0122)	0.747 (0.779)	0.494 (0.541)	0.0222 (0.0328)	0.00192 (0.00347)	0.0136 (0.0208)	0.0762 (0.101)	0.00687 (0.0112)	0.193 (0.236)
amp 20q13 2	416 (67%)	209	1e-05 (2.81e-05)	0.116 (0.149)	0.293 (0.337)	0.0241 (0.0354)	0.00069 (0.00135)	1e-05 (2.81e-05)	0.0647 (0.0869)	1e-05 (2.81e-05)	0.0635 (0.0856)	1e-05 (2.81e-05)
del 3q26 31	65 (10%)	560	1e-05 (2.81e-05)	0.00033 (0.000685)	0.211 (0.253)	0.456 (0.505)	0.0768 (0.102)	1e-05 (2.81e-05)	0.0246 (0.0361)	2e-05 (5.28e-05)	0.348 (0.395)	1e-05 (2.81e-05)
del 6q26	152 (24%)	473	1e-05 (2.81e-05)	0.0138 (0.0212)	0.637 (0.678)	0.2 (0.243)	0.0217 (0.0323)	7e-05 (0.000164)	0.00598 (0.00986)	0.0157 (0.0239)	0.0933 (0.123)	0.0513 (0.0701)
del 12q23 1	110 (18%)	515	1e-05 (2.81e-05)	0.00113 (0.00214)	0.215 (0.257)	0.553 (0.599)	0.00033 (0.000685)	1e-05 (2.81e-05)	0.0512 (0.0701)	0.00034 (0.000704)	0.0107 (0.0169)	0.133 (0.169)
del 14q23 3	187 (30%)	438	1e-05 (2.81e-05)	0.00222 (0.00397)	0.637 (0.678)	0.104 (0.136)	0.0264 (0.0384)	1e-05 (2.81e-05)	0.388 (0.437)	1e-05 (2.81e-05)	0.0683 (0.0915)	1e-05 (2.81e-05)
del xq21 33	98 (16%)	527	1e-05 (2.81e-05)	6e-05 (0.000143)	0.337 (0.384)	0.229 (0.273)	0.00027 (0.000569)	0.00565 (0.00938)	0.00839 (0.0134)	0.00015 (0.000333)	0.203 (0.246)	0.0705 (0.0941)
amp 6q21	111 (18%)	514	1e-05 (2.81e-05)	0.00085 (0.00164)	0.0557 (0.0754)	0.492 (0.541)	0.106 (0.138)	1e-05 (2.81e-05)	0.261 (0.305)	1e-05 (2.81e-05)	0.187 (0.229)	0.00018 (0.000394)
amp 9p13 3	132 (21%)	493	3e-05 (7.62e-05)	0.0943 (0.124)	0.21 (0.253)	0.329 (0.377)	0.0228 (0.0338)	0.0283 (0.0408)	0.128 (0.163)	0.336 (0.383)	0.0268 (0.0389)	0.0251 (0.0367)
amp 10q26 13	119 (19%)	506	1e-05 (2.81e-05)	0.62 (0.664)	0.42 (0.47)	0.239 (0.282)	0.981 (0.986)	0.00123 (0.0023)	0.187 (0.229)	0.00081 (0.00158)	0.0303 (0.0432)	0.00251 (0.00446)
amp 11p13	138 (22%)	487	1e-05 (2.81e-05)	0.00188 (0.0034)	0.264 (0.308)	0.955 (0.966)	0.431 (0.48)	0.0422 (0.0586)	0.637 (0.678)	0.00099 (0.0019)	0.0576 (0.0779)	0.0196 (0.0293)
del 3q11 1	98 (16%)	527	1e-05 (2.81e-05)	3e-05 (7.62e-05)	0.255 (0.299)	0.29 (0.335)	0.107 (0.14)	1e-05 (2.81e-05)	0.328 (0.376)	7e-05 (0.000164)	0.571 (0.614)	0.0116 (0.0181)
del 6q16 3	147 (24%)	478	1e-05 (2.81e-05)	0.0126 (0.0195)	0.515 (0.562)	0.61 (0.654)	0.00315 (0.00544)	0.00028 (0.000589)	0.15 (0.189)	0.00155 (0.00287)	0.0689 (0.0921)	0.0526 (0.0718)
del 12p13 1	113 (18%)	512	1e-05 (2.81e-05)	0.0075 (0.0121)	0.367 (0.415)	0.721 (0.755)	0.156 (0.196)	1e-05 (2.81e-05)	0.455 (0.504)	1e-05 (2.81e-05)	0.418 (0.468)	7e-05 (0.000164)
amp 10q22 2	125 (20%)	500	1e-05 (2.81e-05)	0.0163 (0.0246)	0.806 (0.837)	0.301 (0.346)	0.528 (0.574)	0.00031 (0.000649)	0.676 (0.713)	0.142 (0.18)	0.00115 (0.00217)	0.325 (0.373)
del 1q44	46 (7%)	579	0.00681 (0.0111)	0.125 (0.16)	0.167 (0.208)	0.202 (0.245)	0.0436 (0.0604)	0.0489 (0.0674)	0.0402 (0.0562)	0.168 (0.209)	0.494 (0.541)	0.108 (0.14)
del 17q24 3	103 (16%)	522	1e-05 (2.81e-05)	0.0114 (0.0178)	0.647 (0.687)	0.657 (0.695)	0.0727 (0.0968)	5e-05 (0.000121)	0.0716 (0.0955)	0.0336 (0.0473)	0.534 (0.579)	0.62 (0.664)
del 20p12 1	72 (12%)	553	1e-05 (2.81e-05)	0.105 (0.137)	0.0829 (0.11)	0.627 (0.67)	0.0162 (0.0245)	0.0008 (0.00156)	0.104 (0.136)	0.0024 (0.00428)	0.395 (0.444)	0.476 (0.524)
amp 8p11 21	272 (44%)	353	0.00389 (0.00661)	0.0126 (0.0195)	0.658 (0.695)	0.631 (0.674)	0.143 (0.18)	0.074 (0.0982)	0.0316 (0.0449)	0.238 (0.282)	0.795 (0.827)	0.246 (0.289)
del 2q32 1	87 (14%)	538	0.00052 (0.00105)	0.0408 (0.0569)	0.899 (0.917)	0.236 (0.28)	0.277 (0.321)	0.13 (0.166)	0.22 (0.263)	0.018 (0.0271)	0.516 (0.562)	0.522 (0.567)
amp 9p24 1	91 (15%)	534	0.211 (0.253)	0.554 (0.599)	0.953 (0.965)	1 (1.00)	0.208 (0.251)	0.354 (0.401)	0.0368 (0.0518)	0.64 (0.68)	0.0249 (0.0365)	0.164 (0.204)
amp 12q15	161 (26%)	464	1e-05 (2.81e-05)	0.0682 (0.0915)	0.833 (0.86)	0.291 (0.336)	0.846 (0.87)	0.279 (0.324)	0.0733 (0.0975)	0.0192 (0.0288)	0.183 (0.225)	0.316 (0.363)
del 1q44	43 (7%)	582	0.0323 (0.0457)	0.0357 (0.0502)	0.117 (0.15)	0.23 (0.274)	0.71 (0.744)	0.0926 (0.122)	0.407 (0.457)	0.864 (0.886)	0.837 (0.864)	0.88 (0.9)

'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 1(1P36.22) MUTATED	40	25	32	4
AMP PEAK 1(1P36.22) WILD-TYPE	111	73	150	190

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 = 0.00247 (Fisher's exact test), Q value = 0.0044

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 1(1P36.22) MUTATED	40	37	16
AMP PEAK 1(1P36.22) WILD-TYPE	201	124	159

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

'amp_1p36.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S3. Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 1(1P36.22) MUTATED	37	24	11	19	6
AMP PEAK 1(1P36.22) WILD-TYPE	94	92	87	102	124

Figure S3. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.06

Table S4. Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 1(1P36.22) MUTATED	33	48	18
AMP PEAK 1(1P36.22) WILD-TYPE	134	230	154

Figure S4. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1p36.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00033

Table S5. Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 1(1P36.22) MUTATED	34	29	17	13	6
AMP PEAK 1(1P36.22) WILD-TYPE	93	114	147	81	83

Figure S5. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.042

Table S6. Gene #1: 'amp_1p36.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 1(1P36.22) MUTATED	25	33	12	6	7
AMP PEAK 1(1P36.22) WILD-TYPE	98	122	109	41	66

Figure S6. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1p36.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.036

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 1(1P36.22) MUTATED	12	29	18	11	13
AMP PEAK 1(1P36.22) WILD-TYPE	39	95	126	97	79

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

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S8. Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 2(1P34.2) MUTATED	24	30	36	5
AMP PEAK 2(1P34.2) WILD-TYPE	127	68	146	189

Figure S8. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 0.00172 (Fisher's exact test), Q value = 0.0032

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 2(1P34.2) MUTATED	34	38	17
AMP PEAK 2(1P34.2) WILD-TYPE	207	123	158

Figure S9. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S10. Gene #2: 'amp_1p34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 2(1P34.2) MUTATED	29	26	6	22	8
AMP PEAK 2(1P34.2) WILD-TYPE	102	90	92	99	122

Figure S10. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.024

Table S11. Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 2(1P34.2) MUTATED	28	22	15	19	10
AMP PEAK 2(1P34.2) WILD-TYPE	99	121	149	75	79

Figure S11. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0021

Table S12. Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 2(1P34.2) MUTATED	30	26	13	6	3
AMP PEAK 2(1P34.2) WILD-TYPE	93	129	108	41	70

Figure S12. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0011

Table S13. Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 2(1P34.2) MUTATED	14	24	11	10	19
AMP PEAK 2(1P34.2) WILD-TYPE	37	100	133	98	73

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

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S14. Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 3(1Q21.3) MUTATED	75	54	103	17
AMP PEAK 3(1Q21.3) WILD-TYPE	76	44	79	177

Figure S14. Get High-res Image Gene #3: '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 = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 3(1Q21.3) MUTATED	96	100	36
AMP PEAK 3(1Q21.3) WILD-TYPE	145	61	139

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

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 0.021

Table S16. Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 3(1Q21.3) MUTATED	123	39	29
AMP PEAK 3(1Q21.3) WILD-TYPE	150	71	70

Figure S16. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0023

Table S17. Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 3(1Q21.3) MUTATED	74	123	43
AMP PEAK 3(1Q21.3) WILD-TYPE	96	150	110

Figure S17. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S18. Gene #3: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 3(1Q21.3) MUTATED	72	50	37	55	26
AMP PEAK 3(1Q21.3) WILD-TYPE	59	66	61	66	104

Figure S18. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S19. Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 3(1Q21.3) MUTATED	87	113	45
AMP PEAK 3(1Q21.3) WILD-TYPE	80	165	127

Figure S19. Get High-res Image Gene #3: '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 = 2.8e-05

Table S20. Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 3(1Q21.3) MUTATED	75	73	31	45	21
AMP PEAK 3(1Q21.3) WILD-TYPE	52	70	133	49	68

Figure S20. Get High-res Image Gene #3: '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 = 2.8e-05

Table S21. Gene #3: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 3(1Q21.3) MUTATED	67	72	33	14	20
AMP PEAK 3(1Q21.3) WILD-TYPE	56	83	88	33	53

Figure S21. Get High-res Image Gene #3: '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 = 2.8e-05

Table S22. Gene #3: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 3(1Q21.3) MUTATED	26	66	35	34	45
AMP PEAK 3(1Q21.3) WILD-TYPE	25	58	109	74	47

Figure S22. Get High-res Image Gene #3: '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 = 2.8e-05

Table S23. Gene #4: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 4(1Q42.3) MUTATED	81	52	93	18
AMP PEAK 4(1Q42.3) WILD-TYPE	70	46	89	176

Figure S23. Get High-res Image Gene #4: '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 = 2.8e-05

Table S24. Gene #4: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 4(1Q42.3) MUTATED	83	101	44
AMP PEAK 4(1Q42.3) WILD-TYPE	158	60	131

Figure S24. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0456 (Fisher's exact test), Q value = 0.063

Table S25. Gene #4: 'amp_1q42.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 4(1Q42.3) MUTATED	118	41	29
AMP PEAK 4(1Q42.3) WILD-TYPE	155	69	70

Figure S25. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0011

Table S26. Gene #4: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 4(1Q42.3) MUTATED	83	108	43
AMP PEAK 4(1Q42.3) WILD-TYPE	87	165	110

Figure S26. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S27. Gene #4: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 4(1Q42.3) MUTATED	70	38	36	59	31
AMP PEAK 4(1Q42.3) WILD-TYPE	61	78	62	62	99

Figure S27. Get High-res Image Gene #4: '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 = 2.8e-05

Table S28. Gene #4: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 4(1Q42.3) MUTATED	94	97	50
AMP PEAK 4(1Q42.3) WILD-TYPE	73	181	122

Figure S28. Get High-res Image Gene #4: '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 = 2.8e-05

Table S29. Gene #4: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 4(1Q42.3) MUTATED	78	64	25	50	24
AMP PEAK 4(1Q42.3) WILD-TYPE	49	79	139	44	65

Figure S29. Get High-res Image Gene #4: '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 = 2.8e-05

Table S30. Gene #4: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 4(1Q42.3) MUTATED	73	63	33	17	20
AMP PEAK 4(1Q42.3) WILD-TYPE	50	92	88	30	53

Figure S30. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S31. Gene #4: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 4(1Q42.3) MUTATED	30	56	33	38	49
AMP PEAK 4(1Q42.3) WILD-TYPE	21	68	111	70	43

Figure S31. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S32. Gene #5: 'amp_2q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 5(2Q12.2) MUTATED	50	28	68	9
AMP PEAK 5(2Q12.2) WILD-TYPE	101	70	114	185

Figure S32. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S33. Gene #5: 'amp_2q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 5(2Q12.2) MUTATED	57	63	27
AMP PEAK 5(2Q12.2) WILD-TYPE	184	98	148

Figure S33. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q12.2' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S34. Gene #5: 'amp_2q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 5(2Q12.2) MUTATED	60	71	22
AMP PEAK 5(2Q12.2) WILD-TYPE	110	202	131

Figure S34. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_2q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S35. Gene #5: 'amp_2q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 5(2Q12.2) MUTATED	44	22	23	48	16
AMP PEAK 5(2Q12.2) WILD-TYPE	87	94	75	73	114

Figure S35. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_2q12.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S36. Gene #5: 'amp_2q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 5(2Q12.2) MUTATED	62	64	28
AMP PEAK 5(2Q12.2) WILD-TYPE	105	214	144

Figure S36. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_2q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S37. Gene #5: 'amp_2q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 5(2Q12.2) MUTATED	41	36	26	39	12
AMP PEAK 5(2Q12.2) WILD-TYPE	86	107	138	55	77

Figure S37. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_2q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00039

Table S38. Gene #5: 'amp_2q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 5(2Q12.2) MUTATED	49	42	24	9	10
AMP PEAK 5(2Q12.2) WILD-TYPE	74	113	97	38	63

Figure S38. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_2q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S39. Gene #5: 'amp_2q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 5(2Q12.2) MUTATED	15	37	27	17	38
AMP PEAK 5(2Q12.2) WILD-TYPE	36	87	117	91	54

Figure S39. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S40. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 6(3Q26.2) MUTATED	50	65	143	29
AMP PEAK 6(3Q26.2) WILD-TYPE	101	33	39	165

Figure S40. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S41. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 6(3Q26.2) MUTATED	98	117	53
AMP PEAK 6(3Q26.2) WILD-TYPE	143	44	122

Figure S41. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S42. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 6(3Q26.2) MUTATED	111	119	48
AMP PEAK 6(3Q26.2) WILD-TYPE	59	154	105

Figure S42. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S43. Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 6(3Q26.2) MUTATED	68	62	25	86	37
AMP PEAK 6(3Q26.2) WILD-TYPE	63	54	73	35	93

Figure S43. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S44. Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 6(3Q26.2) MUTATED	117	109	58
AMP PEAK 6(3Q26.2) WILD-TYPE	50	169	114

Figure S44. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S45. Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 6(3Q26.2) MUTATED	62	57	60	81	24
AMP PEAK 6(3Q26.2) WILD-TYPE	65	86	104	13	65

Figure S45. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S46. Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 6(3Q26.2) MUTATED	90	71	42	20	21
AMP PEAK 6(3Q26.2) WILD-TYPE	33	84	79	27	52

Figure S46. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S47. Gene #6: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 6(3Q26.2) MUTATED	25	56	50	33	80
AMP PEAK 6(3Q26.2) WILD-TYPE	26	68	94	75	12

Figure S47. Get High-res Image Gene #6: '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 = 2.8e-05

Table S48. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 7(5P15.33) MUTATED	67	28	116	17
AMP PEAK 7(5P15.33) WILD-TYPE	84	70	66	177

Figure S48. Get High-res Image Gene #7: '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 = 2.8e-05

Table S49. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 7(5P15.33) MUTATED	69	106	40
AMP PEAK 7(5P15.33) WILD-TYPE	172	55	135

Figure S49. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00604 (Fisher's exact test), Q value = 0.0099

Table S50. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 7(5P15.33) MUTATED	112	32	25
AMP PEAK 7(5P15.33) WILD-TYPE	161	78	74

Figure S50. Get High-res Image Gene #7: '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 = 2.8e-05

Table S51. Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 7(5P15.33) MUTATED	87	101	34
AMP PEAK 7(5P15.33) WILD-TYPE	83	172	119

Figure S51. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S52. Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 7(5P15.33) MUTATED	67	35	29	67	24
AMP PEAK 7(5P15.33) WILD-TYPE	64	81	69	54	106

Figure S52. Get High-res Image Gene #7: '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 = 2.8e-05

Table S53. Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 7(5P15.33) MUTATED	95	87	44
AMP PEAK 7(5P15.33) WILD-TYPE	72	191	128

Figure S53. Get High-res Image Gene #7: '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 = 2.8e-05

Table S54. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 7(5P15.33) MUTATED	66	42	37	63	18
AMP PEAK 7(5P15.33) WILD-TYPE	61	101	127	31	71

Figure S54. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S55. Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 7(5P15.33) MUTATED	75	58	28	16	23
AMP PEAK 7(5P15.33) WILD-TYPE	48	97	93	31	50

Figure S55. Get High-res Image Gene #7: '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 = 2.8e-05

Table S56. Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 7(5P15.33) MUTATED	24	46	43	24	63
AMP PEAK 7(5P15.33) WILD-TYPE	27	78	101	84	29

Figure S56. Get High-res Image Gene #7: '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 = 2.8e-05

Table S57. Gene #8: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 8(5P13.1) MUTATED	66	31	103	16
AMP PEAK 8(5P13.1) WILD-TYPE	85	67	79	178

Figure S57. Get High-res Image Gene #8: '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 = 2.8e-05

Table S58. Gene #8: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 8(5P13.1) MUTATED	64	94	43
AMP PEAK 8(5P13.1) WILD-TYPE	177	67	132

Figure S58. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S59. Gene #8: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 8(5P13.1) MUTATED	82	89	38
AMP PEAK 8(5P13.1) WILD-TYPE	88	184	115

Figure S59. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S60. Gene #8: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 8(5P13.1) MUTATED	64	29	25	63	28
AMP PEAK 8(5P13.1) WILD-TYPE	67	87	73	58	102

Figure S60. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S61. Gene #8: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 8(5P13.1) MUTATED	87	78	50
AMP PEAK 8(5P13.1) WILD-TYPE	80	200	122

Figure S61. Get High-res Image Gene #8: '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 = 2.8e-05

Table S62. Gene #8: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 8(5P13.1) MUTATED	65	37	37	55	21
AMP PEAK 8(5P13.1) WILD-TYPE	62	106	127	39	68

Figure S62. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S63. Gene #8: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 8(5P13.1) MUTATED	66	52	32	19	20
AMP PEAK 8(5P13.1) WILD-TYPE	57	103	89	28	53

Figure S63. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S64. Gene #8: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 8(5P13.1) MUTATED	22	40	44	28	55
AMP PEAK 8(5P13.1) WILD-TYPE	29	84	100	80	37

Figure S64. Get High-res Image Gene #8: '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 = 2.8e-05

Table S65. Gene #9: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 9(6P21.1) MUTATED	75	40	65	12
AMP PEAK 9(6P21.1) WILD-TYPE	76	58	117	182

Figure S65. Get High-res Image Gene #9: '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 = 2.8e-05

Table S66. Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 9(6P21.1) MUTATED	79	70	27
AMP PEAK 9(6P21.1) WILD-TYPE	162	91	148

Figure S66. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'RPPA_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.035

Table S67. Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
AMP PEAK 9(6P21.1) MUTATED	45	50	29	24
AMP PEAK 9(6P21.1) WILD-TYPE	100	87	107	40

Figure S67. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_6p21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.018

Table S68. Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 9(6P21.1) MUTATED	88	41	19
AMP PEAK 9(6P21.1) WILD-TYPE	185	69	80

Figure S68. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S69. Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 9(6P21.1) MUTATED	56	104	26
AMP PEAK 9(6P21.1) WILD-TYPE	114	169	127

Figure S69. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S70. Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 9(6P21.1) MUTATED	62	42	30	39	13
AMP PEAK 9(6P21.1) WILD-TYPE	69	74	68	82	117

Figure S70. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00039

Table S71. Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 9(6P21.1) MUTATED	61	96	32
AMP PEAK 9(6P21.1) WILD-TYPE	106	182	140

Figure S71. Get High-res Image Gene #9: '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 = 2.8e-05

Table S72. Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 9(6P21.1) MUTATED	67	56	28	26	12
AMP PEAK 9(6P21.1) WILD-TYPE	60	87	136	68	77

Figure S72. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S73. Gene #9: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 9(6P21.1) MUTATED	49	65	21	14	16
AMP PEAK 9(6P21.1) WILD-TYPE	74	90	100	33	57

Figure S73. Get High-res Image Gene #9: '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 = 2.8e-05

Table S74. Gene #9: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 9(6P21.1) MUTATED	26	63	28	22	26
AMP PEAK 9(6P21.1) WILD-TYPE	25	61	116	86	66

Figure S74. Get High-res Image Gene #9: '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 = 2.8e-05

Table S75. Gene #10: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 10(6Q12) MUTATED	61	28	44	8
AMP PEAK 10(6Q12) WILD-TYPE	90	70	138	186

Figure S75. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S76. Gene #10: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 10(6Q12) MUTATED	54	56	17
AMP PEAK 10(6Q12) WILD-TYPE	187	105	158

Figure S76. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.027

Table S77. Gene #10: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 10(6Q12) MUTATED	44	71	23
AMP PEAK 10(6Q12) WILD-TYPE	126	202	130

Figure S77. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S78. Gene #10: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 10(6Q12) MUTATED	48	27	21	31	11
AMP PEAK 10(6Q12) WILD-TYPE	83	89	77	90	119

Figure S78. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.0294 (Fisher's exact test), Q value = 0.042

Table S79. Gene #10: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 10(6Q12) MUTATED	49	60	30
AMP PEAK 10(6Q12) WILD-TYPE	118	218	142

Figure S79. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S80. Gene #10: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 10(6Q12) MUTATED	50	37	20	22	10
AMP PEAK 10(6Q12) WILD-TYPE	77	106	144	72	79

Figure S80. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S81. Gene #10: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 10(6Q12) MUTATED	41	43	15	9	10
AMP PEAK 10(6Q12) WILD-TYPE	82	112	106	38	63

Figure S81. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S82. Gene #10: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 10(6Q12) MUTATED	22	38	18	18	22
AMP PEAK 10(6Q12) WILD-TYPE	29	86	126	90	70

Figure S82. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S83. Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 11(6Q21) MUTATED	59	25	21	6
AMP PEAK 11(6Q21) WILD-TYPE	92	73	161	188

Figure S83. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.0016

Table S84. Gene #11: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 11(6Q21) MUTATED	43	39	16
AMP PEAK 11(6Q21) WILD-TYPE	198	122	159

Figure S84. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S85. Gene #11: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 11(6Q21) MUTATED	43	19	19	16	10
AMP PEAK 11(6Q21) WILD-TYPE	88	97	79	105	120

Figure S85. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S86. Gene #11: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 11(6Q21) MUTATED	45	30	19	9	7
AMP PEAK 11(6Q21) WILD-TYPE	82	113	145	85	82

Figure S86. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00039

Table S87. Gene #11: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 11(6Q21) MUTATED	17	32	16	16	9
AMP PEAK 11(6Q21) WILD-TYPE	34	92	128	92	83

Figure S87. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S88. Gene #12: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 12(7P22.3) MUTATED	113	54	135	51
AMP PEAK 12(7P22.3) WILD-TYPE	38	44	47	143

Figure S88. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S89. Gene #12: 'amp_7p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 12(7P22.3) MUTATED	153	108	66
AMP PEAK 12(7P22.3) WILD-TYPE	88	53	109

Figure S89. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S90. Gene #12: 'amp_7p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 12(7P22.3) MUTATED	104	172	62
AMP PEAK 12(7P22.3) WILD-TYPE	66	101	91

Figure S90. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S91. Gene #12: 'amp_7p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 12(7P22.3) MUTATED	93	60	57	76	52
AMP PEAK 12(7P22.3) WILD-TYPE	38	56	41	45	78

Figure S91. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S92. Gene #12: 'amp_7p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 12(7P22.3) MUTATED	111	163	74
AMP PEAK 12(7P22.3) WILD-TYPE	56	115	98

Figure S92. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S93. Gene #12: 'amp_7p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 12(7P22.3) MUTATED	88	92	76	61	31
AMP PEAK 12(7P22.3) WILD-TYPE	39	51	88	33	58

Figure S93. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00068

Table S94. Gene #12: 'amp_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 12(7P22.3) MUTATED	86	94	51	28	37
AMP PEAK 12(7P22.3) WILD-TYPE	37	61	70	19	36

Figure S94. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S95. Gene #12: 'amp_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 12(7P22.3) MUTATED	38	81	72	45	60
AMP PEAK 12(7P22.3) WILD-TYPE	13	43	72	63	32

Figure S95. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S96. Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 13(7P11.2) MUTATED	98	51	139	51
AMP PEAK 13(7P11.2) WILD-TYPE	53	47	43	143

Figure S96. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S97. Gene #13: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 13(7P11.2) MUTATED	147	105	64
AMP PEAK 13(7P11.2) WILD-TYPE	94	56	111

Figure S97. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S98. Gene #13: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 13(7P11.2) MUTATED	102	163	61
AMP PEAK 13(7P11.2) WILD-TYPE	68	110	92

Figure S98. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S99. Gene #13: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 13(7P11.2) MUTATED	85	59	53	78	51
AMP PEAK 13(7P11.2) WILD-TYPE	46	57	45	43	79

Figure S99. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00033

Table S100. Gene #13: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 13(7P11.2) MUTATED	105	157	71
AMP PEAK 13(7P11.2) WILD-TYPE	62	121	101

Figure S100. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S101. Gene #13: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 13(7P11.2) MUTATED	78	92	74	59	30
AMP PEAK 13(7P11.2) WILD-TYPE	49	51	90	35	59

Figure S101. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S102. Gene #13: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 13(7P11.2) MUTATED	82	91	49	27	32
AMP PEAK 13(7P11.2) WILD-TYPE	41	64	72	20	41

Figure S102. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S103. Gene #13: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 13(7P11.2) MUTATED	35	78	68	42	58
AMP PEAK 13(7P11.2) WILD-TYPE	16	46	76	66	34

Figure S103. Get High-res Image Gene #13: '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 = 2.8e-05

Table S104. Gene #14: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 14(7Q21.2) MUTATED	91	39	137	50
AMP PEAK 14(7Q21.2) WILD-TYPE	60	59	45	144

Figure S104. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S105. Gene #14: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 14(7Q21.2) MUTATED	131	98	63
AMP PEAK 14(7Q21.2) WILD-TYPE	110	63	112

Figure S105. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00357 (Fisher's exact test), Q value = 0.0061

Table S106. Gene #14: 'amp_7q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 14(7Q21.2) MUTATED	98	146	61
AMP PEAK 14(7Q21.2) WILD-TYPE	72	127	92

Figure S106. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.025

Table S107. Gene #14: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 14(7Q21.2) MUTATED	74	54	55	70	52
AMP PEAK 14(7Q21.2) WILD-TYPE	57	62	43	51	78

Figure S107. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.02

Table S108. Gene #14: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 14(7Q21.2) MUTATED	94	147	71
AMP PEAK 14(7Q21.2) WILD-TYPE	73	131	101

Figure S108. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.0026

Table S109. Gene #14: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 14(7Q21.2) MUTATED	69	78	77	58	30
AMP PEAK 14(7Q21.2) WILD-TYPE	58	65	87	36	59

Figure S109. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0072 (Fisher's exact test), Q value = 0.012

Table S110. Gene #14: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 14(7Q21.2) MUTATED	75	81	46	26	34
AMP PEAK 14(7Q21.2) WILD-TYPE	48	74	75	21	39

Figure S110. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00634 (Fisher's exact test), Q value = 0.01

Table S111. Gene #14: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 14(7Q21.2) MUTATED	28	69	67	41	57
AMP PEAK 14(7Q21.2) WILD-TYPE	23	55	77	67	35

Figure S111. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S112. Gene #15: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 15(8P23.1) MUTATED	44	48	37	100
AMP PEAK 15(8P23.1) WILD-TYPE	107	50	145	94

Figure S112. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S113. Gene #15: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 15(8P23.1) MUTATED	116	37	53
AMP PEAK 15(8P23.1) WILD-TYPE	125	124	122

Figure S113. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S114. Gene #15: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 15(8P23.1) MUTATED	34	124	61
AMP PEAK 15(8P23.1) WILD-TYPE	136	149	92

Figure S114. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S115. Gene #15: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 15(8P23.1) MUTATED	37	60	44	20	58
AMP PEAK 15(8P23.1) WILD-TYPE	94	56	54	101	72

Figure S115. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S116. Gene #15: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 15(8P23.1) MUTATED	41	125	58
AMP PEAK 15(8P23.1) WILD-TYPE	126	153	114

Figure S116. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0021

Table S117. Gene #15: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 15(8P23.1) MUTATED	43	64	65	18	34
AMP PEAK 15(8P23.1) WILD-TYPE	84	79	99	76	55

Figure S117. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0023

Table S118. Gene #15: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 15(8P23.1) MUTATED	26	69	40	18	28
AMP PEAK 15(8P23.1) WILD-TYPE	97	86	81	29	45

Figure S118. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S119. Gene #15: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 15(8P23.1) MUTATED	12	53	57	43	16
AMP PEAK 15(8P23.1) WILD-TYPE	39	71	87	65	76

Figure S119. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 0.00389 (Fisher's exact test), Q value = 0.0066

Table S120. Gene #16: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 16(8P11.21) MUTATED	50	50	74	98
AMP PEAK 16(8P11.21) WILD-TYPE	101	48	108	96

Figure S120. Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.019

Table S121. Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 16(8P11.21) MUTATED	119	68	61
AMP PEAK 16(8P11.21) WILD-TYPE	122	93	114

Figure S121. Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.045

Table S122. Gene #16: 'amp_8p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 16(8P11.21) MUTATED	69	136	63
AMP PEAK 16(8P11.21) WILD-TYPE	98	142	109

Figure S122. Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S123. Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 17(8Q24.21) MUTATED	124	65	147	118
AMP PEAK 17(8Q24.21) WILD-TYPE	27	33	35	76

Figure S123. Get High-res Image Gene #17: '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 = 2.8e-05

Table S124. Gene #17: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 17(8Q24.21) MUTATED	183	134	100
AMP PEAK 17(8Q24.21) WILD-TYPE	58	27	75

Figure S124. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0023

Table S125. Gene #17: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 17(8Q24.21) MUTATED	133	207	94
AMP PEAK 17(8Q24.21) WILD-TYPE	37	66	59

Figure S125. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S126. Gene #17: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 17(8Q24.21) MUTATED	111	84	73	94	72
AMP PEAK 17(8Q24.21) WILD-TYPE	20	32	25	27	58

Figure S126. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S127. Gene #17: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 17(8Q24.21) MUTATED	142	209	98
AMP PEAK 17(8Q24.21) WILD-TYPE	25	69	74

Figure S127. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S128. Gene #17: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 17(8Q24.21) MUTATED	105	123	92	77	52
AMP PEAK 17(8Q24.21) WILD-TYPE	22	20	72	17	37

Figure S128. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S129. Gene #17: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 17(8Q24.21) MUTATED	107	116	71	33	50
AMP PEAK 17(8Q24.21) WILD-TYPE	16	39	50	14	23

Figure S129. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00047

Table S130. Gene #17: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 17(8Q24.21) MUTATED	43	101	91	68	74
AMP PEAK 17(8Q24.21) WILD-TYPE	8	23	53	40	18

Figure S130. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.052

Table S131. Gene #18: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 18(9P24.1) MUTATED	34	36	19
AMP PEAK 18(9P24.1) WILD-TYPE	133	242	153

Figure S131. Get High-res Image Gene #18: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.036

Table S132. Gene #18: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 18(9P24.1) MUTATED	27	19	11	3	11
AMP PEAK 18(9P24.1) WILD-TYPE	96	136	110	44	62

Figure S132. Get High-res Image Gene #18: 'amp_9p24.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S133. Gene #19: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 19(9P13.3) MUTATED	46	29	33	24
AMP PEAK 19(9P13.3) WILD-TYPE	105	69	149	170

Figure S133. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.034

Table S134. Gene #19: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 19(9P13.3) MUTATED	39	67	21
AMP PEAK 19(9P13.3) WILD-TYPE	131	206	132

Figure S134. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0283 (Fisher's exact test), Q value = 0.041

Table S135. Gene #19: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 19(9P13.3) MUTATED	36	28	23	24	16
AMP PEAK 19(9P13.3) WILD-TYPE	95	88	75	97	114

Figure S135. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.039

Table S136. Gene #19: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 19(9P13.3) MUTATED	35	40	18	6	13
AMP PEAK 19(9P13.3) WILD-TYPE	88	115	103	41	60

Figure S136. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.037

Table S137. Gene #19: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 19(9P13.3) MUTATED	16	36	23	18	19
AMP PEAK 19(9P13.3) WILD-TYPE	35	88	121	90	73

Figure S137. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S138. Gene #20: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 20(9Q34.3) MUTATED	58	21	75	31
AMP PEAK 20(9Q34.3) WILD-TYPE	93	77	107	163

Figure S138. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.00761 (Fisher's exact test), Q value = 0.012

Table S139. Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 20(9Q34.3) MUTATED	70	61	39
AMP PEAK 20(9Q34.3) WILD-TYPE	171	100	136

Figure S139. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.033

Table S140. Gene #20: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 20(9Q34.3) MUTATED	60	84	33
AMP PEAK 20(9Q34.3) WILD-TYPE	110	189	120

Figure S140. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0035

Table S141. Gene #20: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 20(9Q34.3) MUTATED	52	32	26	43	24
AMP PEAK 20(9Q34.3) WILD-TYPE	79	84	72	78	106

Figure S141. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.021

Table S142. Gene #20: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 20(9Q34.3) MUTATED	61	83	38
AMP PEAK 20(9Q34.3) WILD-TYPE	106	195	134

Figure S142. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.011

Table S143. Gene #20: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 20(9Q34.3) MUTATED	47	48	25	15	13
AMP PEAK 20(9Q34.3) WILD-TYPE	76	107	96	32	60

Figure S143. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S144. Gene #21: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 21(10P11.22) MUTATED	68	44	45	12
AMP PEAK 21(10P11.22) WILD-TYPE	83	54	137	182

Figure S144. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S145. Gene #21: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 21(10P11.22) MUTATED	75	54	28
AMP PEAK 21(10P11.22) WILD-TYPE	166	107	147

Figure S145. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CNMF'

P value = 0.0261 (Fisher's exact test), Q value = 0.038

Table S146. Gene #21: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 21(10P11.22) MUTATED	45	88	31
AMP PEAK 21(10P11.22) WILD-TYPE	125	185	122

Figure S146. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0033

Table S147. Gene #21: 'amp_10p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 21(10P11.22) MUTATED	50	36	28	28	22
AMP PEAK 21(10P11.22) WILD-TYPE	81	80	70	93	108

Figure S147. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S148. Gene #21: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 21(10P11.22) MUTATED	57	42	28	21	18
AMP PEAK 21(10P11.22) WILD-TYPE	70	101	136	73	71

Figure S148. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.0067

Table S149. Gene #21: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 21(10P11.22) MUTATED	37	56	30	9	10
AMP PEAK 21(10P11.22) WILD-TYPE	86	99	91	38	63

Figure S149. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.019

Table S150. Gene #21: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 21(10P11.22) MUTATED	16	48	29	27	22
AMP PEAK 21(10P11.22) WILD-TYPE	35	76	115	81	70

Figure S150. Get High-res Image Gene #21: '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 = 2.8e-05

Table S151. Gene #22: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 22(10Q22.2) MUTATED	38	46	28	13
AMP PEAK 22(10Q22.2) WILD-TYPE	113	52	154	181

Figure S151. Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'METHLYATION_CNMF'

P value = 0.0163 (Fisher's exact test), Q value = 0.025

Table S152. Gene #22: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 22(10Q22.2) MUTATED	58	35	23
AMP PEAK 22(10Q22.2) WILD-TYPE	183	126	152

Figure S152. Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S153. Gene #22: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 22(10Q22.2) MUTATED	36	35	10	17	22
AMP PEAK 22(10Q22.2) WILD-TYPE	95	81	88	104	108

Figure S153. Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.0022

Table S154. Gene #22: 'amp_10q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 22(10Q22.2) MUTATED	21	49	17	8	9
AMP PEAK 22(10Q22.2) WILD-TYPE	102	106	104	39	64

Figure S154. Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10q26.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S155. Gene #23: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 23(10Q26.13) MUTATED	42	35	24	18
AMP PEAK 23(10Q26.13) WILD-TYPE	109	63	158	176

Figure S155. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.0023

Table S156. Gene #23: 'amp_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 23(10Q26.13) MUTATED	38	27	11	14	22
AMP PEAK 23(10Q26.13) WILD-TYPE	93	89	87	107	108

Figure S156. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0016

Table S157. Gene #23: 'amp_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 23(10Q26.13) MUTATED	37	30	26	7	17
AMP PEAK 23(10Q26.13) WILD-TYPE	90	113	138	87	72

Figure S157. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.043

Table S158. Gene #23: 'amp_10q26.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 23(10Q26.13) MUTATED	17	42	23	5	12
AMP PEAK 23(10Q26.13) WILD-TYPE	106	113	98	42	61

Figure S158. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00251 (Fisher's exact test), Q value = 0.0045

Table S159. Gene #23: 'amp_10q26.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 23(10Q26.13) MUTATED	11	32	25	25	6
AMP PEAK 23(10Q26.13) WILD-TYPE	40	92	119	83	86

Figure S159. Get High-res Image Gene #23: '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 = 2.8e-05

Table S160. Gene #24: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 24(11P13) MUTATED	49	29	47	13
AMP PEAK 24(11P13) WILD-TYPE	102	69	135	181

Figure S160. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00188 (Fisher's exact test), Q value = 0.0034

Table S161. Gene #24: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 24(11P13) MUTATED	47	52	30
AMP PEAK 24(11P13) WILD-TYPE	194	109	145

Figure S161. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.059

Table S162. Gene #24: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 24(11P13) MUTATED	38	21	15	34	26
AMP PEAK 24(11P13) WILD-TYPE	93	95	83	87	104

Figure S162. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0019

Table S163. Gene #24: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 24(11P13) MUTATED	42	28	25	27	13
AMP PEAK 24(11P13) WILD-TYPE	85	115	139	67	76

Figure S163. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0196 (Fisher's exact test), Q value = 0.029

Table S164. Gene #24: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 24(11P13) MUTATED	18	28	23	20	27
AMP PEAK 24(11P13) WILD-TYPE	33	96	121	88	65

Figure S164. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S165. Gene #25: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 25(11Q13.3) MUTATED	63	36	103	16
AMP PEAK 25(11Q13.3) WILD-TYPE	88	62	79	178

Figure S165. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S166. Gene #25: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 25(11Q13.3) MUTATED	73	91	41
AMP PEAK 25(11Q13.3) WILD-TYPE	168	70	134

Figure S166. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.058

Table S167. Gene #25: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 25(11Q13.3) MUTATED	92	47	26
AMP PEAK 25(11Q13.3) WILD-TYPE	181	63	73

Figure S167. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S168. Gene #25: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 25(11Q13.3) MUTATED	96	90	25
AMP PEAK 25(11Q13.3) WILD-TYPE	74	183	128

Figure S168. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S169. Gene #25: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 25(11Q13.3) MUTATED	58	35	25	75	18
AMP PEAK 25(11Q13.3) WILD-TYPE	73	81	73	46	112

Figure S169. Get High-res Image Gene #25: '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 = 2.8e-05

Table S170. Gene #25: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 25(11Q13.3) MUTATED	88	89	38
AMP PEAK 25(11Q13.3) WILD-TYPE	79	189	134

Figure S170. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S171. Gene #25: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 25(11Q13.3) MUTATED	49	53	35	67	11
AMP PEAK 25(11Q13.3) WILD-TYPE	78	90	129	27	78

Figure S171. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S172. Gene #25: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 25(11Q13.3) MUTATED	72	60	30	22	7
AMP PEAK 25(11Q13.3) WILD-TYPE	51	95	91	25	66

Figure S172. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S173. Gene #25: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 25(11Q13.3) MUTATED	21	47	39	18	66
AMP PEAK 25(11Q13.3) WILD-TYPE	30	77	105	90	26

Figure S173. Get High-res Image Gene #25: '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 = 2.8e-05

Table S174. Gene #26: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 26(12P12.1) MUTATED	45	45	89	28
AMP PEAK 26(12P12.1) WILD-TYPE	106	53	93	166

Figure S174. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S175. Gene #26: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 26(12P12.1) MUTATED	75	78	45
AMP PEAK 26(12P12.1) WILD-TYPE	166	83	130

Figure S175. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0033

Table S176. Gene #26: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 26(12P12.1) MUTATED	75	78	44
AMP PEAK 26(12P12.1) WILD-TYPE	95	195	109

Figure S176. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S177. Gene #26: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 26(12P12.1) MUTATED	54	30	23	59	31
AMP PEAK 26(12P12.1) WILD-TYPE	77	86	75	62	99

Figure S177. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00047

Table S178. Gene #26: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 26(12P12.1) MUTATED	77	80	47
AMP PEAK 26(12P12.1) WILD-TYPE	90	198	125

Figure S178. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.0036

Table S179. Gene #26: 'amp_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 26(12P12.1) MUTATED	44	43	49	47	21
AMP PEAK 26(12P12.1) WILD-TYPE	83	100	115	47	68

Figure S179. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0013

Table S180. Gene #26: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 26(12P12.1) MUTATED	62	50	35	12	19
AMP PEAK 26(12P12.1) WILD-TYPE	61	105	86	35	54

Figure S180. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.0045

Table S181. Gene #26: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 26(12P12.1) MUTATED	17	42	46	26	47
AMP PEAK 26(12P12.1) WILD-TYPE	34	82	98	82	45

Figure S181. Get High-res Image Gene #26: '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 = 2.8e-05

Table S182. Gene #27: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 27(12Q15) MUTATED	39	41	55	26
AMP PEAK 27(12Q15) WILD-TYPE	112	57	127	168

Figure S182. Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.029

Table S183. Gene #27: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 27(12Q15) MUTATED	40	25	50	26	17
AMP PEAK 27(12Q15) WILD-TYPE	87	118	114	68	72

Figure S183. Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S184. Gene #28: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 28(13Q12.3) MUTATED	114	13	57	32
AMP PEAK 28(13Q12.3) WILD-TYPE	37	85	125	162

Figure S184. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.04

Table S185. Gene #28: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 28(13Q12.3) MUTATED	92	59	46
AMP PEAK 28(13Q12.3) WILD-TYPE	149	102	129

Figure S185. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S186. Gene #28: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 28(13Q12.3) MUTATED	43	122	42
AMP PEAK 28(13Q12.3) WILD-TYPE	127	151	111

Figure S186. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S187. Gene #28: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 28(13Q12.3) MUTATED	65	37	50	23	32
AMP PEAK 28(13Q12.3) WILD-TYPE	66	79	48	98	98

Figure S187. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.037

Table S188. Gene #28: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 28(13Q12.3) MUTATED	50	112	51
AMP PEAK 28(13Q12.3) WILD-TYPE	117	166	121

Figure S188. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S189. Gene #28: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 28(13Q12.3) MUTATED	72	68	38	9	26
AMP PEAK 28(13Q12.3) WILD-TYPE	55	75	126	85	63

Figure S189. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.02

Table S190. Gene #28: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 28(13Q12.3) MUTATED	34	63	30	21	27
AMP PEAK 28(13Q12.3) WILD-TYPE	89	92	91	26	46

Figure S190. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S191. Gene #28: 'amp_13q12.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 28(13Q12.3) MUTATED	30	49	47	40	9
AMP PEAK 28(13Q12.3) WILD-TYPE	21	75	97	68	83

Figure S191. Get High-res Image Gene #28: '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 = 2.8e-05

Table S192. Gene #29: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 29(13Q22.1) MUTATED	125	15	64	39
AMP PEAK 29(13Q22.1) WILD-TYPE	26	83	118	155

Figure S192. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00063

Table S193. Gene #29: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 29(13Q22.1) MUTATED	97	77	47
AMP PEAK 29(13Q22.1) WILD-TYPE	144	84	128

Figure S193. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.0022

Table S194. Gene #29: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 29(13Q22.1) MUTATED	65	124	42
AMP PEAK 29(13Q22.1) WILD-TYPE	105	149	111

Figure S194. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S195. Gene #29: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 29(13Q22.1) MUTATED	83	35	52	31	30
AMP PEAK 29(13Q22.1) WILD-TYPE	48	81	46	90	100

Figure S195. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.042

Table S196. Gene #29: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 29(13Q22.1) MUTATED	69	117	52
AMP PEAK 29(13Q22.1) WILD-TYPE	98	161	120

Figure S196. Get High-res Image Gene #29: '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 = 2.8e-05

Table S197. Gene #29: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 29(13Q22.1) MUTATED	78	76	38	19	27
AMP PEAK 29(13Q22.1) WILD-TYPE	49	67	126	75	62

Figure S197. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.0082

Table S198. Gene #29: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 29(13Q22.1) MUTATED	49	69	29	20	32
AMP PEAK 29(13Q22.1) WILD-TYPE	74	86	92	27	41

Figure S198. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S199. Gene #29: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 29(13Q22.1) MUTATED	38	56	46	40	19
AMP PEAK 29(13Q22.1) WILD-TYPE	13	68	98	68	73

Figure S199. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S200. Gene #30: 'amp_14q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 30(14Q13.3) MUTATED	26	13	69	5
AMP PEAK 30(14Q13.3) WILD-TYPE	125	85	113	189

Figure S200. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S201. Gene #30: 'amp_14q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 30(14Q13.3) MUTATED	34	52	21
AMP PEAK 30(14Q13.3) WILD-TYPE	207	109	154

Figure S201. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S202. Gene #30: 'amp_14q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 30(14Q13.3) MUTATED	53	45	12
AMP PEAK 30(14Q13.3) WILD-TYPE	117	228	141

Figure S202. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S203. Gene #30: 'amp_14q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 30(14Q13.3) MUTATED	29	15	13	46	7
AMP PEAK 30(14Q13.3) WILD-TYPE	102	101	85	75	123

Figure S203. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S204. Gene #30: 'amp_14q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 30(14Q13.3) MUTATED	52	36	23
AMP PEAK 30(14Q13.3) WILD-TYPE	115	242	149

Figure S204. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S205. Gene #30: 'amp_14q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 30(14Q13.3) MUTATED	21	26	11	41	12
AMP PEAK 30(14Q13.3) WILD-TYPE	106	117	153	53	77

Figure S205. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S206. Gene #30: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 30(14Q13.3) MUTATED	41	25	19	9	5
AMP PEAK 30(14Q13.3) WILD-TYPE	82	130	102	38	68

Figure S206. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S207. Gene #30: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 30(14Q13.3) MUTATED	9	24	12	13	41
AMP PEAK 30(14Q13.3) WILD-TYPE	42	100	132	95	51

Figure S207. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S208. Gene #31: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 31(15Q26.1) MUTATED	57	40	58	13
AMP PEAK 31(15Q26.1) WILD-TYPE	94	58	124	181

Figure S208. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

P value = 0.00347 (Fisher's exact test), Q value = 0.006

Table S209. Gene #31: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 31(15Q26.1) MUTATED	71	54	32
AMP PEAK 31(15Q26.1) WILD-TYPE	170	107	143

Figure S209. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'RPPA_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0038

Table S210. Gene #31: 'amp_15q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
AMP PEAK 31(15Q26.1) MUTATED	37	43	22	25
AMP PEAK 31(15Q26.1) WILD-TYPE	108	94	114	39

Figure S210. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_15q26.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00651 (Fisher's exact test), Q value = 0.011

Table S211. Gene #31: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 31(15Q26.1) MUTATED	75	37	15
AMP PEAK 31(15Q26.1) WILD-TYPE	198	73	84

Figure S211. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S212. Gene #31: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 31(15Q26.1) MUTATED	57	82	20
AMP PEAK 31(15Q26.1) WILD-TYPE	113	191	133

Figure S212. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S213. Gene #31: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 31(15Q26.1) MUTATED	58	34	25	32	10
AMP PEAK 31(15Q26.1) WILD-TYPE	73	82	73	89	120

Figure S213. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.017

Table S214. Gene #31: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 31(15Q26.1) MUTATED	57	75	34
AMP PEAK 31(15Q26.1) WILD-TYPE	110	203	138

Figure S214. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S215. Gene #31: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 31(15Q26.1) MUTATED	52	43	40	20	11
AMP PEAK 31(15Q26.1) WILD-TYPE	75	100	124	74	78

Figure S215. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 8e-04

Table S216. Gene #31: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 31(15Q26.1) MUTATED	20	52	33	22	21
AMP PEAK 31(15Q26.1) WILD-TYPE	31	72	111	86	71

Figure S216. Get High-res Image Gene #31: '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 = 2.8e-05

Table S217. Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 32(17Q12) MUTATED	85	44	79	14
AMP PEAK 32(17Q12) WILD-TYPE	66	54	103	180

Figure S217. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S218. Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 32(17Q12) MUTATED	94	72	42
AMP PEAK 32(17Q12) WILD-TYPE	147	89	133

Figure S218. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S219. Gene #32: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 32(17Q12) MUTATED	66	116	30
AMP PEAK 32(17Q12) WILD-TYPE	104	157	123

Figure S219. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S220. Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 32(17Q12) MUTATED	69	47	28	41	27
AMP PEAK 32(17Q12) WILD-TYPE	62	69	70	80	103

Figure S220. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.017

Table S221. Gene #32: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 32(17Q12) MUTATED	70	102	46
AMP PEAK 32(17Q12) WILD-TYPE	97	176	126

Figure S221. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S222. Gene #32: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 32(17Q12) MUTATED	64	59	47	29	19
AMP PEAK 32(17Q12) WILD-TYPE	63	84	117	65	70

Figure S222. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00416 (Fisher's exact test), Q value = 0.007

Table S223. Gene #32: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 32(17Q12) MUTATED	23	58	48	27	28
AMP PEAK 32(17Q12) WILD-TYPE	28	66	96	81	64

Figure S223. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S224. Gene #33: 'amp_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 33(18P11.32) MUTATED	45	31	84	18
AMP PEAK 33(18P11.32) WILD-TYPE	106	67	98	176

Figure S224. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S225. Gene #33: 'amp_18p11.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 33(18P11.32) MUTATED	52	74	42
AMP PEAK 33(18P11.32) WILD-TYPE	189	87	133

Figure S225. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.003

Table S226. Gene #33: 'amp_18p11.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 33(18P11.32) MUTATED	60	85	28
AMP PEAK 33(18P11.32) WILD-TYPE	110	188	125

Figure S226. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S227. Gene #33: 'amp_18p11.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 33(18P11.32) MUTATED	50	37	24	46	16
AMP PEAK 33(18P11.32) WILD-TYPE	81	79	74	75	114

Figure S227. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00053

Table S228. Gene #33: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 33(18P11.32) MUTATED	66	77	33
AMP PEAK 33(18P11.32) WILD-TYPE	101	201	139

Figure S228. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S229. Gene #33: 'amp_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 33(18P11.32) MUTATED	52	40	32	41	11
AMP PEAK 33(18P11.32) WILD-TYPE	75	103	132	53	78

Figure S229. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0016

Table S230. Gene #33: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 33(18P11.32) MUTATED	51	50	26	13	12
AMP PEAK 33(18P11.32) WILD-TYPE	72	105	95	34	61

Figure S230. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00078

Table S231. Gene #33: 'amp_18p11.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 33(18P11.32) MUTATED	19	41	31	21	40
AMP PEAK 33(18P11.32) WILD-TYPE	32	83	113	87	52

Figure S231. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S232. Gene #34: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 34(18Q11.2) MUTATED	71	40	65	22
AMP PEAK 34(18Q11.2) WILD-TYPE	80	58	117	172

Figure S232. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00513 (Fisher's exact test), Q value = 0.0086

Table S233. Gene #34: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 34(18Q11.2) MUTATED	49	103	35
AMP PEAK 34(18Q11.2) WILD-TYPE	121	170	118

Figure S233. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S234. Gene #34: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 34(18Q11.2) MUTATED	63	52	20	31	21
AMP PEAK 34(18Q11.2) WILD-TYPE	68	64	78	90	109

Figure S234. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.046

Table S235. Gene #34: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 34(18Q11.2) MUTATED	51	102	43
AMP PEAK 34(18Q11.2) WILD-TYPE	116	176	129

Figure S235. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S236. Gene #34: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 34(18Q11.2) MUTATED	60	50	43	21	22
AMP PEAK 34(18Q11.2) WILD-TYPE	67	93	121	73	67

Figure S236. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.0095

Table S237. Gene #34: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 34(18Q11.2) MUTATED	34	64	27	17	18
AMP PEAK 34(18Q11.2) WILD-TYPE	89	91	94	30	55

Figure S237. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00746 (Fisher's exact test), Q value = 0.012

Table S238. Gene #34: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 34(18Q11.2) MUTATED	21	51	40	28	20
AMP PEAK 34(18Q11.2) WILD-TYPE	30	73	104	80	72

Figure S238. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S239. Gene #35: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 35(19Q12) MUTATED	72	40	60	13
AMP PEAK 35(19Q12) WILD-TYPE	79	58	122	181

Figure S239. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S240. Gene #35: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 35(19Q12) MUTATED	60	71	42
AMP PEAK 35(19Q12) WILD-TYPE	181	90	133

Figure S240. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00084

Table S241. Gene #35: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
AMP PEAK 35(19Q12) MUTATED	61	31	29	18
AMP PEAK 35(19Q12) WILD-TYPE	84	106	107	46

Figure S241. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0017

Table S242. Gene #35: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 35(19Q12) MUTATED	97	23	19
AMP PEAK 35(19Q12) WILD-TYPE	176	87	80

Figure S242. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S243. Gene #35: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 35(19Q12) MUTATED	69	27	25	28	27
AMP PEAK 35(19Q12) WILD-TYPE	62	89	73	93	103

Figure S243. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.032

Table S244. Gene #35: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 35(19Q12) MUTATED	64	75	45
AMP PEAK 35(19Q12) WILD-TYPE	103	203	127

Figure S244. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S245. Gene #35: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 35(19Q12) MUTATED	83	37	24	23	17
AMP PEAK 35(19Q12) WILD-TYPE	44	106	140	71	72

Figure S245. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S246. Gene #35: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 35(19Q12) MUTATED	34	40	29	33	22
AMP PEAK 35(19Q12) WILD-TYPE	17	84	115	75	70

Figure S246. Get High-res Image Gene #35: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S247. Gene #36: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 36(19Q13.43) MUTATED	57	32	55	20
AMP PEAK 36(19Q13.43) WILD-TYPE	94	66	127	174

Figure S247. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.016

Table S248. Gene #36: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 36(19Q13.43) MUTATED	67	53	33
AMP PEAK 36(19Q13.43) WILD-TYPE	174	108	142

Figure S248. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'RPPA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.02

Table S249. Gene #36: 'amp_19q13.43' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
AMP PEAK 36(19Q13.43) MUTATED	50	27	29	12
AMP PEAK 36(19Q13.43) WILD-TYPE	95	110	107	52

Figure S249. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q13.43' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.032

Table S250. Gene #36: 'amp_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 36(19Q13.43) MUTATED	51	79	32
AMP PEAK 36(19Q13.43) WILD-TYPE	116	199	140

Figure S250. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S251. Gene #36: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 36(19Q13.43) MUTATED	52	44	29	23	14
AMP PEAK 36(19Q13.43) WILD-TYPE	75	99	135	71	75

Figure S251. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00882 (Fisher's exact test), Q value = 0.014

Table S252. Gene #36: 'amp_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 36(19Q13.43) MUTATED	42	48	21	12	13
AMP PEAK 36(19Q13.43) WILD-TYPE	81	107	100	35	60

Figure S252. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00744 (Fisher's exact test), Q value = 0.012

Table S253. Gene #36: 'amp_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 36(19Q13.43) MUTATED	22	39	34	19	22
AMP PEAK 36(19Q13.43) WILD-TYPE	29	85	110	89	70

Figure S253. Get High-res Image Gene #36: 'amp_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S254. Gene #37: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 37(20Q13.2) MUTATED	137	77	139	63
AMP PEAK 37(20Q13.2) WILD-TYPE	14	21	43	131

Figure S254. Get High-res Image Gene #37: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 0.035

Table S255. Gene #37: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
AMP PEAK 37(20Q13.2) MUTATED	190	75	54
AMP PEAK 37(20Q13.2) WILD-TYPE	83	35	45

Figure S255. Get High-res Image Gene #37: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0014

Table S256. Gene #37: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 37(20Q13.2) MUTATED	105	205	90
AMP PEAK 37(20Q13.2) WILD-TYPE	65	68	63

Figure S256. Get High-res Image Gene #37: '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 = 2.8e-05

Table S257. Gene #37: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 37(20Q13.2) MUTATED	117	82	58	68	75
AMP PEAK 37(20Q13.2) WILD-TYPE	14	34	40	53	55

Figure S257. Get High-res Image Gene #37: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S258. Gene #37: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 37(20Q13.2) MUTATED	119	102	95	49	45
AMP PEAK 37(20Q13.2) WILD-TYPE	8	41	69	45	44

Figure S258. Get High-res Image Gene #37: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S259. Gene #37: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 37(20Q13.2) MUTATED	47	96	82	68	49
AMP PEAK 37(20Q13.2) WILD-TYPE	4	28	62	40	43

Figure S259. Get High-res Image Gene #37: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S260. Gene #38: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
AMP PEAK 38(XQ28) MUTATED	41	22	70	22
AMP PEAK 38(XQ28) WILD-TYPE	110	76	112	172

Figure S260. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S261. Gene #38: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
AMP PEAK 38(XQ28) MUTATED	65	59	21
AMP PEAK 38(XQ28) WILD-TYPE	176	102	154

Figure S261. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S262. Gene #38: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
AMP PEAK 38(XQ28) MUTATED	66	68	13
AMP PEAK 38(XQ28) WILD-TYPE	104	205	140

Figure S262. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S263. Gene #38: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
AMP PEAK 38(XQ28) MUTATED	25	25	31	50	16
AMP PEAK 38(XQ28) WILD-TYPE	106	91	67	71	114

Figure S263. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S264. Gene #38: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
AMP PEAK 38(XQ28) MUTATED	61	68	24
AMP PEAK 38(XQ28) WILD-TYPE	106	210	148

Figure S264. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S265. Gene #38: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
AMP PEAK 38(XQ28) MUTATED	30	43	21	45	14
AMP PEAK 38(XQ28) WILD-TYPE	97	100	143	49	75

Figure S265. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S266. Gene #38: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
AMP PEAK 38(XQ28) MUTATED	47	43	16	15	11
AMP PEAK 38(XQ28) WILD-TYPE	76	112	105	32	62

Figure S266. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S267. Gene #38: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
AMP PEAK 38(XQ28) MUTATED	8	40	21	19	44
AMP PEAK 38(XQ28) WILD-TYPE	43	84	123	89	48

Figure S267. Get High-res Image Gene #38: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S268. Gene #39: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 1(1P36.11) MUTATED	80	51	71	8
DEL PEAK 1(1P36.11) WILD-TYPE	71	47	111	186

Figure S268. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S269. Gene #39: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 1(1P36.11) MUTATED	87	70	35
DEL PEAK 1(1P36.11) WILD-TYPE	154	91	140

Figure S269. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.00534 (Fisher's exact test), Q value = 0.0089

Table S270. Gene #39: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
DEL PEAK 1(1P36.11) MUTATED	47	54	28	23
DEL PEAK 1(1P36.11) WILD-TYPE	98	83	108	41

Figure S270. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0047

Table S271. Gene #39: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 1(1P36.11) MUTATED	88	45	19
DEL PEAK 1(1P36.11) WILD-TYPE	185	65	80

Figure S271. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S272. Gene #39: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 1(1P36.11) MUTATED	63	113	27
DEL PEAK 1(1P36.11) WILD-TYPE	107	160	126

Figure S272. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S273. Gene #39: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 1(1P36.11) MUTATED	62	49	32	41	19
DEL PEAK 1(1P36.11) WILD-TYPE	69	67	66	80	111

Figure S273. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S274. Gene #39: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 1(1P36.11) MUTATED	68	102	37
DEL PEAK 1(1P36.11) WILD-TYPE	99	176	135

Figure S274. Get High-res Image Gene #39: '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 = 2.8e-05

Table S275. Gene #39: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 1(1P36.11) MUTATED	66	55	41	30	15
DEL PEAK 1(1P36.11) WILD-TYPE	61	88	123	64	74

Figure S275. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0034

Table S276. Gene #39: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 1(1P36.11) MUTATED	52	64	27	12	22
DEL PEAK 1(1P36.11) WILD-TYPE	71	91	94	35	51

Figure S276. Get High-res Image Gene #39: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S277. Gene #39: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 1(1P36.11) MUTATED	27	58	36	25	31
DEL PEAK 1(1P36.11) WILD-TYPE	24	66	108	83	61

Figure S277. Get High-res Image Gene #39: '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 = 2.8e-05

Table S278. Gene #40: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 2(1P13.2) MUTATED	61	25	65	5
DEL PEAK 2(1P13.2) WILD-TYPE	90	73	117	189

Figure S278. Get High-res Image Gene #40: '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 = 2.8e-05

Table S279. Gene #40: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 2(1P13.2) MUTATED	66	64	17
DEL PEAK 2(1P13.2) WILD-TYPE	175	97	158

Figure S279. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S280. Gene #40: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 2(1P13.2) MUTATED	55	76	19
DEL PEAK 2(1P13.2) WILD-TYPE	115	197	134

Figure S280. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S281. Gene #40: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 2(1P13.2) MUTATED	44	25	28	41	12
DEL PEAK 2(1P13.2) WILD-TYPE	87	91	70	80	118

Figure S281. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00341 (Fisher's exact test), Q value = 0.0059

Table S282. Gene #40: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 2(1P13.2) MUTATED	52	74	28
DEL PEAK 2(1P13.2) WILD-TYPE	115	204	144

Figure S282. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S283. Gene #40: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 2(1P13.2) MUTATED	41	46	25	32	10
DEL PEAK 2(1P13.2) WILD-TYPE	86	97	139	62	79

Figure S283. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.024

Table S284. Gene #40: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 2(1P13.2) MUTATED	41	48	26	7	13
DEL PEAK 2(1P13.2) WILD-TYPE	82	107	95	40	60

Figure S284. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.03

Table S285. Gene #40: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 2(1P13.2) MUTATED	15	38	32	18	32
DEL PEAK 2(1P13.2) WILD-TYPE	36	86	112	90	60

Figure S285. Get High-res Image Gene #40: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.00681 (Fisher's exact test), Q value = 0.011

Table S286. Gene #41: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 3(1Q44) MUTATED	16	7	18	5
DEL PEAK 3(1Q44) WILD-TYPE	135	91	164	189

Figure S286. Get High-res Image Gene #41: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'MRNASEQ_CNMF'

P value = 0.0436 (Fisher's exact test), Q value = 0.06

Table S287. Gene #41: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 3(1Q44) MUTATED	14	26	5
DEL PEAK 3(1Q44) WILD-TYPE	156	247	148

Figure S287. Get High-res Image Gene #41: 'del_1q44' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.067

Table S288. Gene #41: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 3(1Q44) MUTATED	17	10	4	9	5
DEL PEAK 3(1Q44) WILD-TYPE	114	106	94	112	125

Figure S288. Get High-res Image Gene #41: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.056

Table S289. Gene #41: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 3(1Q44) MUTATED	12	27	6
DEL PEAK 3(1Q44) WILD-TYPE	155	251	166

Figure S289. Get High-res Image Gene #41: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'CN_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.046

Table S290. Gene #42: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 4(1Q44) MUTATED	10	8	19	6
DEL PEAK 4(1Q44) WILD-TYPE	141	90	163	188

Figure S290. Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.05

Table S291. Gene #42: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 4(1Q44) MUTATED	21	16	6
DEL PEAK 4(1Q44) WILD-TYPE	220	145	169

Figure S291. Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S292. Gene #43: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 5(2Q22.1) MUTATED	31	28	60	7
DEL PEAK 5(2Q22.1) WILD-TYPE	120	70	122	187

Figure S292. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S293. Gene #43: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 5(2Q22.1) MUTATED	32	66	21
DEL PEAK 5(2Q22.1) WILD-TYPE	209	95	154

Figure S293. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.035

Table S294. Gene #43: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 5(2Q22.1) MUTATED	67	20	12
DEL PEAK 5(2Q22.1) WILD-TYPE	206	90	87

Figure S294. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S295. Gene #43: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 5(2Q22.1) MUTATED	65	39	15
DEL PEAK 5(2Q22.1) WILD-TYPE	105	234	138

Figure S295. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S296. Gene #43: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 5(2Q22.1) MUTATED	26	21	11	52	9
DEL PEAK 5(2Q22.1) WILD-TYPE	105	95	87	69	121

Figure S296. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S297. Gene #43: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 5(2Q22.1) MUTATED	64	39	22
DEL PEAK 5(2Q22.1) WILD-TYPE	103	239	150

Figure S297. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S298. Gene #43: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 5(2Q22.1) MUTATED	33	18	21	46	7
DEL PEAK 5(2Q22.1) WILD-TYPE	94	125	143	48	82

Figure S298. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S299. Gene #43: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 5(2Q22.1) MUTATED	48	26	12	9	13
DEL PEAK 5(2Q22.1) WILD-TYPE	75	129	109	38	60

Figure S299. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S300. Gene #43: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 5(2Q22.1) MUTATED	11	25	17	9	46
DEL PEAK 5(2Q22.1) WILD-TYPE	40	99	127	99	46

Figure S300. Get High-res Image Gene #43: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0011

Table S301. Gene #44: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 6(2Q32.1) MUTATED	29	20	26	12
DEL PEAK 6(2Q32.1) WILD-TYPE	122	78	156	182

Figure S301. Get High-res Image Gene #44: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.057

Table S302. Gene #44: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 6(2Q32.1) MUTATED	33	30	16
DEL PEAK 6(2Q32.1) WILD-TYPE	208	131	159

Figure S302. Get High-res Image Gene #44: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.027

Table S303. Gene #44: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 6(2Q32.1) MUTATED	29	14	17	15	11
DEL PEAK 6(2Q32.1) WILD-TYPE	98	129	147	79	78

Figure S303. Get High-res Image Gene #44: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S304. Gene #45: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 7(2Q33.3) MUTATED	23	18	39	5
DEL PEAK 7(2Q33.3) WILD-TYPE	128	80	143	189

Figure S304. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S305. Gene #45: 'del_2q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 7(2Q33.3) MUTATED	28	39	15
DEL PEAK 7(2Q33.3) WILD-TYPE	213	122	160

Figure S305. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q33.3' versus 'MRNASEQ_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.0029

Table S306. Gene #45: 'del_2q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 7(2Q33.3) MUTATED	36	34	12
DEL PEAK 7(2Q33.3) WILD-TYPE	134	239	141

Figure S306. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00266 (Fisher's exact test), Q value = 0.0047

Table S307. Gene #45: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 7(2Q33.3) MUTATED	22	15	10	27	8
DEL PEAK 7(2Q33.3) WILD-TYPE	109	101	88	94	122

Figure S307. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S308. Gene #45: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 7(2Q33.3) MUTATED	39	29	15
DEL PEAK 7(2Q33.3) WILD-TYPE	128	249	157

Figure S308. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S309. Gene #45: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 7(2Q33.3) MUTATED	23	15	15	25	5
DEL PEAK 7(2Q33.3) WILD-TYPE	104	128	149	69	84

Figure S309. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0051

Table S310. Gene #45: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 7(2Q33.3) MUTATED	6	16	15	9	25
DEL PEAK 7(2Q33.3) WILD-TYPE	45	108	129	99	67

Figure S310. Get High-res Image Gene #45: 'del_2q33.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S311. Gene #46: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 8(2Q37.2) MUTATED	33	25	54	10
DEL PEAK 8(2Q37.2) WILD-TYPE	118	73	128	184

Figure S311. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S312. Gene #46: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 8(2Q37.2) MUTATED	38	56	23
DEL PEAK 8(2Q37.2) WILD-TYPE	203	105	152

Figure S312. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0013

Table S313. Gene #46: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 8(2Q37.2) MUTATED	51	48	21
DEL PEAK 8(2Q37.2) WILD-TYPE	119	225	132

Figure S313. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S314. Gene #46: 'del_2q37.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 8(2Q37.2) MUTATED	36	22	14	38	10
DEL PEAK 8(2Q37.2) WILD-TYPE	95	94	84	83	120

Figure S314. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 0.00139 (Fisher's exact test), Q value = 0.0026

Table S315. Gene #46: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 8(2Q37.2) MUTATED	48	48	24
DEL PEAK 8(2Q37.2) WILD-TYPE	119	230	148

Figure S315. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S316. Gene #46: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 8(2Q37.2) MUTATED	33	25	19	36	7
DEL PEAK 8(2Q37.2) WILD-TYPE	94	118	145	58	82

Figure S316. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.038

Table S317. Gene #46: 'del_2q37.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 8(2Q37.2) MUTATED	36	33	15	8	15
DEL PEAK 8(2Q37.2) WILD-TYPE	87	122	106	39	58

Figure S317. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00035

Table S318. Gene #46: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 8(2Q37.2) MUTATED	11	26	20	15	35
DEL PEAK 8(2Q37.2) WILD-TYPE	40	98	124	93	57

Figure S318. Get High-res Image Gene #46: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S319. Gene #47: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 9(3P26.2) MUTATED	81	38	121	10
DEL PEAK 9(3P26.2) WILD-TYPE	70	60	61	184

Figure S319. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S320. Gene #47: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 9(3P26.2) MUTATED	86	103	46
DEL PEAK 9(3P26.2) WILD-TYPE	155	58	129

Figure S320. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S321. Gene #47: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 9(3P26.2) MUTATED	96	108	34
DEL PEAK 9(3P26.2) WILD-TYPE	74	165	119

Figure S321. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S322. Gene #47: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 9(3P26.2) MUTATED	59	35	35	84	25
DEL PEAK 9(3P26.2) WILD-TYPE	72	81	63	37	105

Figure S322. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S323. Gene #47: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 9(3P26.2) MUTATED	100	104	43
DEL PEAK 9(3P26.2) WILD-TYPE	67	174	129

Figure S323. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S324. Gene #47: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 9(3P26.2) MUTATED	63	56	39	74	15
DEL PEAK 9(3P26.2) WILD-TYPE	64	87	125	20	74

Figure S324. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S325. Gene #47: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 9(3P26.2) MUTATED	79	64	38	20	15
DEL PEAK 9(3P26.2) WILD-TYPE	44	91	83	27	58

Figure S325. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S326. Gene #47: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 9(3P26.2) MUTATED	28	50	35	30	73
DEL PEAK 9(3P26.2) WILD-TYPE	23	74	109	78	19

Figure S326. Get High-res Image Gene #47: 'del_3p26.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S327. Gene #48: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 10(3P14.2) MUTATED	79	44	134	25
DEL PEAK 10(3P14.2) WILD-TYPE	72	54	48	169

Figure S327. Get High-res Image Gene #48: '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 = 2.8e-05

Table S328. Gene #48: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 10(3P14.2) MUTATED	104	115	50
DEL PEAK 10(3P14.2) WILD-TYPE	137	46	125

Figure S328. Get High-res Image Gene #48: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.053

Table S329. Gene #48: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 10(3P14.2) MUTATED	135	41	38
DEL PEAK 10(3P14.2) WILD-TYPE	138	69	61

Figure S329. Get High-res Image Gene #48: 'del_3p14.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S330. Gene #48: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 10(3P14.2) MUTATED	110	122	38
DEL PEAK 10(3P14.2) WILD-TYPE	60	151	115

Figure S330. Get High-res Image Gene #48: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S331. Gene #48: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 10(3P14.2) MUTATED	68	43	39	95	25
DEL PEAK 10(3P14.2) WILD-TYPE	63	73	59	26	105

Figure S331. Get High-res Image Gene #48: '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 = 2.8e-05

Table S332. Gene #48: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 10(3P14.2) MUTATED	112	117	50
DEL PEAK 10(3P14.2) WILD-TYPE	55	161	122

Figure S332. Get High-res Image Gene #48: '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 = 2.8e-05

Table S333. Gene #48: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 10(3P14.2) MUTATED	68	64	47	83	17
DEL PEAK 10(3P14.2) WILD-TYPE	59	79	117	11	72

Figure S333. Get High-res Image Gene #48: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S334. Gene #48: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 10(3P14.2) MUTATED	87	71	45	17	25
DEL PEAK 10(3P14.2) WILD-TYPE	36	84	76	30	48

Figure S334. Get High-res Image Gene #48: '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 = 2.8e-05

Table S335. Gene #48: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 10(3P14.2) MUTATED	26	61	45	31	82
DEL PEAK 10(3P14.2) WILD-TYPE	25	63	99	77	10

Figure S335. Get High-res Image Gene #48: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S336. Gene #49: 'del_3q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 11(3Q11.1) MUTATED	53	11	30	4
DEL PEAK 11(3Q11.1) WILD-TYPE	98	87	152	190

Figure S336. Get High-res Image Gene #49: 'del_3q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q11.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S337. Gene #49: 'del_3q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 11(3Q11.1) MUTATED	47	34	11
DEL PEAK 11(3Q11.1) WILD-TYPE	194	127	164

Figure S337. Get High-res Image Gene #49: 'del_3q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S338. Gene #49: 'del_3q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 11(3Q11.1) MUTATED	35	9	21	18	10
DEL PEAK 11(3Q11.1) WILD-TYPE	96	107	77	103	120

Figure S338. Get High-res Image Gene #49: 'del_3q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S339. Gene #49: 'del_3q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 11(3Q11.1) MUTATED	34	27	11	16	9
DEL PEAK 11(3Q11.1) WILD-TYPE	93	116	153	78	80

Figure S339. Get High-res Image Gene #49: 'del_3q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.018

Table S340. Gene #49: 'del_3q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 11(3Q11.1) MUTATED	17	20	16	15	16
DEL PEAK 11(3Q11.1) WILD-TYPE	34	104	128	93	76

Figure S340. Get High-res Image Gene #49: 'del_3q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S341. Gene #50: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 12(3Q26.31) MUTATED	47	4	10	4
DEL PEAK 12(3Q26.31) WILD-TYPE	104	94	172	190

Figure S341. Get High-res Image Gene #50: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00068

Table S342. Gene #50: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 12(3Q26.31) MUTATED	34	21	6
DEL PEAK 12(3Q26.31) WILD-TYPE	207	140	169

Figure S342. Get High-res Image Gene #50: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S343. Gene #50: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 12(3Q26.31) MUTATED	28	5	19	4	8
DEL PEAK 12(3Q26.31) WILD-TYPE	103	111	79	117	122

Figure S343. Get High-res Image Gene #50: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.036

Table S344. Gene #50: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 12(3Q26.31) MUTATED	16	38	10
DEL PEAK 12(3Q26.31) WILD-TYPE	151	240	162

Figure S344. Get High-res Image Gene #50: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S345. Gene #50: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 12(3Q26.31) MUTATED	28	22	6	2	6
DEL PEAK 12(3Q26.31) WILD-TYPE	99	121	158	92	83

Figure S345. Get High-res Image Gene #50: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S346. Gene #50: 'del_3q26.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 12(3Q26.31) MUTATED	18	15	8	11	2
DEL PEAK 12(3Q26.31) WILD-TYPE	33	109	136	97	90

Figure S346. Get High-res Image Gene #50: '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 = 2.8e-05

Table S347. Gene #51: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 13(4P16.3) MUTATED	101	62	93	15
DEL PEAK 13(4P16.3) WILD-TYPE	50	36	89	179

Figure S347. Get High-res Image Gene #51: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S348. Gene #51: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 13(4P16.3) MUTATED	96	95	61
DEL PEAK 13(4P16.3) WILD-TYPE	145	66	114

Figure S348. Get High-res Image Gene #51: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.046

Table S349. Gene #51: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 13(4P16.3) MUTATED	87	118	56
DEL PEAK 13(4P16.3) WILD-TYPE	83	155	97

Figure S349. Get High-res Image Gene #51: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S350. Gene #51: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 13(4P16.3) MUTATED	78	43	34	68	38
DEL PEAK 13(4P16.3) WILD-TYPE	53	73	64	53	92

Figure S350. Get High-res Image Gene #51: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S351. Gene #51: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 13(4P16.3) MUTATED	100	106	64
DEL PEAK 13(4P16.3) WILD-TYPE	67	172	108

Figure S351. Get High-res Image Gene #51: '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 = 2.8e-05

Table S352. Gene #51: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 13(4P16.3) MUTATED	79	67	41	53	30
DEL PEAK 13(4P16.3) WILD-TYPE	48	76	123	41	59

Figure S352. Get High-res Image Gene #51: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S353. Gene #51: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 13(4P16.3) MUTATED	76	66	49	27	16
DEL PEAK 13(4P16.3) WILD-TYPE	47	89	72	20	57

Figure S353. Get High-res Image Gene #51: '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 = 2.8e-05

Table S354. Gene #51: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 13(4P16.3) MUTATED	37	55	41	48	53
DEL PEAK 13(4P16.3) WILD-TYPE	14	69	103	60	39

Figure S354. Get High-res Image Gene #51: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S355. Gene #52: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 14(4P15.2) MUTATED	99	66	92	12
DEL PEAK 14(4P15.2) WILD-TYPE	52	32	90	182

Figure S355. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S356. Gene #52: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 14(4P15.2) MUTATED	96	93	60
DEL PEAK 14(4P15.2) WILD-TYPE	145	68	115

Figure S356. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00571 (Fisher's exact test), Q value = 0.0095

Table S357. Gene #52: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 14(4P15.2) MUTATED	88	118	52
DEL PEAK 14(4P15.2) WILD-TYPE	82	155	101

Figure S357. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S358. Gene #52: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 14(4P15.2) MUTATED	75	44	33	69	37
DEL PEAK 14(4P15.2) WILD-TYPE	56	72	65	52	93

Figure S358. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S359. Gene #52: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 14(4P15.2) MUTATED	101	104	63
DEL PEAK 14(4P15.2) WILD-TYPE	66	174	109

Figure S359. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S360. Gene #52: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 14(4P15.2) MUTATED	81	63	39	55	30
DEL PEAK 14(4P15.2) WILD-TYPE	46	80	125	39	59

Figure S360. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S361. Gene #52: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 14(4P15.2) MUTATED	76	64	48	24	16
DEL PEAK 14(4P15.2) WILD-TYPE	47	91	73	23	57

Figure S361. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S362. Gene #52: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 14(4P15.2) MUTATED	36	54	39	44	55
DEL PEAK 14(4P15.2) WILD-TYPE	15	70	105	64	37

Figure S362. Get High-res Image Gene #52: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S363. Gene #53: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 15(4Q22.1) MUTATED	111	71	100	16
DEL PEAK 15(4Q22.1) WILD-TYPE	40	27	82	178

Figure S363. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00051

Table S364. Gene #53: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 15(4Q22.1) MUTATED	126	89	62
DEL PEAK 15(4Q22.1) WILD-TYPE	115	72	113

Figure S364. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0018

Table S365. Gene #53: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 15(4Q22.1) MUTATED	83	147	54
DEL PEAK 15(4Q22.1) WILD-TYPE	87	126	99

Figure S365. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S366. Gene #53: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 15(4Q22.1) MUTATED	81	59	46	61	37
DEL PEAK 15(4Q22.1) WILD-TYPE	50	57	52	60	93

Figure S366. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00733 (Fisher's exact test), Q value = 0.012

Table S367. Gene #53: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 15(4Q22.1) MUTATED	92	136	66
DEL PEAK 15(4Q22.1) WILD-TYPE	75	142	106

Figure S367. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S368. Gene #53: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 15(4Q22.1) MUTATED	82	79	57	46	30
DEL PEAK 15(4Q22.1) WILD-TYPE	45	64	107	48	59

Figure S368. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.027

Table S369. Gene #53: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 15(4Q22.1) MUTATED	70	80	48	24	27
DEL PEAK 15(4Q22.1) WILD-TYPE	53	75	73	23	46

Figure S369. Get High-res Image Gene #53: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00515 (Fisher's exact test), Q value = 0.0086

Table S370. Gene #53: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 15(4Q22.1) MUTATED	31	71	54	47	46
DEL PEAK 15(4Q22.1) WILD-TYPE	20	53	90	61	46

Figure S370. Get High-res Image Gene #53: '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 = 2.8e-05

Table S371. Gene #54: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 16(4Q34.3) MUTATED	109	73	101	17
DEL PEAK 16(4Q34.3) WILD-TYPE	42	25	81	177

Figure S371. Get High-res Image Gene #54: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.0099

Table S372. Gene #54: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 16(4Q34.3) MUTATED	124	89	68
DEL PEAK 16(4Q34.3) WILD-TYPE	117	72	107

Figure S372. Get High-res Image Gene #54: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0213 (Fisher's exact test), Q value = 0.032

Table S373. Gene #54: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 16(4Q34.3) MUTATED	84	145	60
DEL PEAK 16(4Q34.3) WILD-TYPE	86	128	93

Figure S373. Get High-res Image Gene #54: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S374. Gene #54: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 16(4Q34.3) MUTATED	89	63	41	56	40
DEL PEAK 16(4Q34.3) WILD-TYPE	42	53	57	65	90

Figure S374. Get High-res Image Gene #54: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.035

Table S375. Gene #54: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 16(4Q34.3) MUTATED	91	138	69
DEL PEAK 16(4Q34.3) WILD-TYPE	76	140	103

Figure S375. Get High-res Image Gene #54: '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 = 2.8e-05

Table S376. Gene #54: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 16(4Q34.3) MUTATED	90	80	56	42	30
DEL PEAK 16(4Q34.3) WILD-TYPE	37	63	108	52	59

Figure S376. Get High-res Image Gene #54: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.016

Table S377. Gene #54: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 16(4Q34.3) MUTATED	68	86	52	26	25
DEL PEAK 16(4Q34.3) WILD-TYPE	55	69	69	21	48

Figure S377. Get High-res Image Gene #54: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S378. Gene #54: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 16(4Q34.3) MUTATED	38	74	54	49	42
DEL PEAK 16(4Q34.3) WILD-TYPE	13	50	90	59	50

Figure S378. Get High-res Image Gene #54: '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 = 2.8e-05

Table S379. Gene #55: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 17(5Q12.1) MUTATED	98	58	119	7
DEL PEAK 17(5Q12.1) WILD-TYPE	53	40	63	187

Figure S379. Get High-res Image Gene #55: '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 = 2.8e-05

Table S380. Gene #55: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 17(5Q12.1) MUTATED	107	118	43
DEL PEAK 17(5Q12.1) WILD-TYPE	134	43	132

Figure S380. Get High-res Image Gene #55: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0035

Table S381. Gene #55: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
DEL PEAK 17(5Q12.1) MUTATED	73	61	40	32
DEL PEAK 17(5Q12.1) WILD-TYPE	72	76	96	32

Figure S381. Get High-res Image Gene #55: 'del_5q12.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00289 (Fisher's exact test), Q value = 0.0051

Table S382. Gene #55: 'del_5q12.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 17(5Q12.1) MUTATED	131	47	28
DEL PEAK 17(5Q12.1) WILD-TYPE	142	63	71

Figure S382. Get High-res Image Gene #55: '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 = 2.8e-05

Table S383. Gene #55: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 17(5Q12.1) MUTATED	99	138	35
DEL PEAK 17(5Q12.1) WILD-TYPE	71	135	118

Figure S383. Get High-res Image Gene #55: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S384. Gene #55: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 17(5Q12.1) MUTATED	95	53	34	72	18
DEL PEAK 17(5Q12.1) WILD-TYPE	36	63	64	49	112

Figure S384. Get High-res Image Gene #55: '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 = 2.8e-05

Table S385. Gene #55: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 17(5Q12.1) MUTATED	105	126	47
DEL PEAK 17(5Q12.1) WILD-TYPE	62	152	125

Figure S385. Get High-res Image Gene #55: '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 = 2.8e-05

Table S386. Gene #55: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 17(5Q12.1) MUTATED	97	70	42	54	15
DEL PEAK 17(5Q12.1) WILD-TYPE	30	73	122	40	74

Figure S386. Get High-res Image Gene #55: '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 = 2.8e-05

Table S387. Gene #55: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 17(5Q12.1) MUTATED	84	80	41	16	27
DEL PEAK 17(5Q12.1) WILD-TYPE	39	75	80	31	46

Figure S387. Get High-res Image Gene #55: '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 = 2.8e-05

Table S388. Gene #55: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 17(5Q12.1) MUTATED	42	64	53	35	54
DEL PEAK 17(5Q12.1) WILD-TYPE	9	60	91	73	38

Figure S388. Get High-res Image Gene #55: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S389. Gene #56: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 18(6P25.3) MUTATED	55	41	74	18
DEL PEAK 18(6P25.3) WILD-TYPE	96	57	108	176

Figure S389. Get High-res Image Gene #56: '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 = 2.8e-05

Table S390. Gene #56: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 18(6P25.3) MUTATED	77	72	32
DEL PEAK 18(6P25.3) WILD-TYPE	164	89	143

Figure S390. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00074

Table S391. Gene #56: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 18(6P25.3) MUTATED	61	90	27
DEL PEAK 18(6P25.3) WILD-TYPE	109	183	126

Figure S391. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S392. Gene #56: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 18(6P25.3) MUTATED	58	42	19	44	15
DEL PEAK 18(6P25.3) WILD-TYPE	73	74	79	77	115

Figure S392. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.0054

Table S393. Gene #56: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 18(6P25.3) MUTATED	60	90	35
DEL PEAK 18(6P25.3) WILD-TYPE	107	188	137

Figure S393. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S394. Gene #56: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 18(6P25.3) MUTATED	55	50	34	33	13
DEL PEAK 18(6P25.3) WILD-TYPE	72	93	130	61	76

Figure S394. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.057

Table S395. Gene #56: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 18(6P25.3) MUTATED	41	60	28	17	18
DEL PEAK 18(6P25.3) WILD-TYPE	82	95	93	30	55

Figure S395. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0012

Table S396. Gene #56: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 18(6P25.3) MUTATED	16	57	35	24	32
DEL PEAK 18(6P25.3) WILD-TYPE	35	67	109	84	60

Figure S396. Get High-res Image Gene #56: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S397. Gene #57: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 19(6Q16.3) MUTATED	33	21	80	13
DEL PEAK 19(6Q16.3) WILD-TYPE	118	77	102	181

Figure S397. Get High-res Image Gene #57: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q16.3' versus 'METHLYATION_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.02

Table S398. Gene #57: 'del_6q16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 19(6Q16.3) MUTATED	53	52	33
DEL PEAK 19(6Q16.3) WILD-TYPE	188	109	142

Figure S398. Get High-res Image Gene #57: 'del_6q16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q16.3' versus 'MRNASEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.0054

Table S399. Gene #57: 'del_6q16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 19(6Q16.3) MUTATED	52	68	23
DEL PEAK 19(6Q16.3) WILD-TYPE	118	205	130

Figure S399. Get High-res Image Gene #57: 'del_6q16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00059

Table S400. Gene #57: 'del_6q16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 19(6Q16.3) MUTATED	34	37	16	39	17
DEL PEAK 19(6Q16.3) WILD-TYPE	97	79	82	82	113

Figure S400. Get High-res Image Gene #57: 'del_6q16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00155 (Fisher's exact test), Q value = 0.0029

Table S401. Gene #57: 'del_6q16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 19(6Q16.3) MUTATED	36	32	36	32	9
DEL PEAK 19(6Q16.3) WILD-TYPE	91	111	128	62	80

Figure S401. Get High-res Image Gene #57: 'del_6q16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S402. Gene #58: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 20(6Q26) MUTATED	40	28	70	14
DEL PEAK 20(6Q26) WILD-TYPE	111	70	112	180

Figure S402. Get High-res Image Gene #58: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.021

Table S403. Gene #58: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 20(6Q26) MUTATED	53	53	35
DEL PEAK 20(6Q26) WILD-TYPE	188	108	140

Figure S403. Get High-res Image Gene #58: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.032

Table S404. Gene #58: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 20(6Q26) MUTATED	51	69	26
DEL PEAK 20(6Q26) WILD-TYPE	119	204	127

Figure S404. Get High-res Image Gene #58: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S405. Gene #58: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 20(6Q26) MUTATED	46	35	12	33	20
DEL PEAK 20(6Q26) WILD-TYPE	85	81	86	88	110

Figure S405. Get High-res Image Gene #58: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.00598 (Fisher's exact test), Q value = 0.0099

Table S406. Gene #58: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 20(6Q26) MUTATED	54	66	30
DEL PEAK 20(6Q26) WILD-TYPE	113	212	142

Figure S406. Get High-res Image Gene #58: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.024

Table S407. Gene #58: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 20(6Q26) MUTATED	37	33	39	30	11
DEL PEAK 20(6Q26) WILD-TYPE	90	110	125	64	78

Figure S407. Get High-res Image Gene #58: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S408. Gene #59: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 21(7Q31.1) MUTATED	39	38	40	10
DEL PEAK 21(7Q31.1) WILD-TYPE	112	60	142	184

Figure S408. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S409. Gene #59: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 21(7Q31.1) MUTATED	56	45	18
DEL PEAK 21(7Q31.1) WILD-TYPE	185	116	157

Figure S409. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0039

Table S410. Gene #59: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 21(7Q31.1) MUTATED	46	60	18
DEL PEAK 21(7Q31.1) WILD-TYPE	124	213	135

Figure S410. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00068

Table S411. Gene #59: 'del_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 21(7Q31.1) MUTATED	37	28	12	33	14
DEL PEAK 21(7Q31.1) WILD-TYPE	94	88	86	88	116

Figure S411. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.017

Table S412. Gene #59: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 21(7Q31.1) MUTATED	46	53	25
DEL PEAK 21(7Q31.1) WILD-TYPE	121	225	147

Figure S412. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00091 (Fisher's exact test), Q value = 0.0017

Table S413. Gene #59: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 21(7Q31.1) MUTATED	38	30	21	24	11
DEL PEAK 21(7Q31.1) WILD-TYPE	89	113	143	70	78

Figure S413. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.019

Table S414. Gene #59: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 21(7Q31.1) MUTATED	34	38	20	12	7
DEL PEAK 21(7Q31.1) WILD-TYPE	89	117	101	35	66

Figure S414. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0029

Table S415. Gene #59: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 21(7Q31.1) MUTATED	14	38	20	15	24
DEL PEAK 21(7Q31.1) WILD-TYPE	37	86	124	93	68

Figure S415. Get High-res Image Gene #59: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S416. Gene #60: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 22(7Q36.3) MUTATED	49	46	63	7
DEL PEAK 22(7Q36.3) WILD-TYPE	102	52	119	187

Figure S416. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S417. Gene #60: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 22(7Q36.3) MUTATED	58	65	33
DEL PEAK 22(7Q36.3) WILD-TYPE	183	96	142

Figure S417. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00084

Table S418. Gene #60: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 22(7Q36.3) MUTATED	61	75	25
DEL PEAK 22(7Q36.3) WILD-TYPE	109	198	128

Figure S418. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S419. Gene #60: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 22(7Q36.3) MUTATED	57	36	13	40	15
DEL PEAK 22(7Q36.3) WILD-TYPE	74	80	85	81	115

Figure S419. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S420. Gene #60: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 22(7Q36.3) MUTATED	68	68	27
DEL PEAK 22(7Q36.3) WILD-TYPE	99	210	145

Figure S420. Get High-res Image Gene #60: '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 = 2.8e-05

Table S421. Gene #60: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 22(7Q36.3) MUTATED	54	37	29	33	10
DEL PEAK 22(7Q36.3) WILD-TYPE	73	106	135	61	79

Figure S421. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0011

Table S422. Gene #60: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 22(7Q36.3) MUTATED	50	44	22	17	14
DEL PEAK 22(7Q36.3) WILD-TYPE	73	111	99	30	59

Figure S422. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.0045

Table S423. Gene #60: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 22(7Q36.3) MUTATED	21	41	33	19	33
DEL PEAK 22(7Q36.3) WILD-TYPE	30	83	111	89	59

Figure S423. Get High-res Image Gene #60: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S424. Gene #61: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 23(8P23.2) MUTATED	71	25	105	13
DEL PEAK 23(8P23.2) WILD-TYPE	80	73	77	181

Figure S424. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S425. Gene #61: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 23(8P23.2) MUTATED	74	86	42
DEL PEAK 23(8P23.2) WILD-TYPE	167	75	133

Figure S425. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.025

Table S426. Gene #61: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 23(8P23.2) MUTATED	106	26	33
DEL PEAK 23(8P23.2) WILD-TYPE	167	84	66

Figure S426. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S427. Gene #61: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 23(8P23.2) MUTATED	84	85	36
DEL PEAK 23(8P23.2) WILD-TYPE	86	188	117

Figure S427. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S428. Gene #61: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 23(8P23.2) MUTATED	68	31	26	63	17
DEL PEAK 23(8P23.2) WILD-TYPE	63	85	72	58	113

Figure S428. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S429. Gene #61: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 23(8P23.2) MUTATED	89	87	36
DEL PEAK 23(8P23.2) WILD-TYPE	78	191	136

Figure S429. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S430. Gene #61: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 23(8P23.2) MUTATED	61	47	30	57	17
DEL PEAK 23(8P23.2) WILD-TYPE	66	96	134	37	72

Figure S430. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S431. Gene #61: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 23(8P23.2) MUTATED	67	48	35	16	19
DEL PEAK 23(8P23.2) WILD-TYPE	56	107	86	31	54

Figure S431. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S432. Gene #61: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 23(8P23.2) MUTATED	30	40	37	24	54
DEL PEAK 23(8P23.2) WILD-TYPE	21	84	107	84	38

Figure S432. Get High-res Image Gene #61: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S433. Gene #62: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 24(9P23) MUTATED	93	72	119	18
DEL PEAK 24(9P23) WILD-TYPE	58	26	63	176

Figure S433. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.0052

Table S434. Gene #62: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 24(9P23) MUTATED	115	96	72
DEL PEAK 24(9P23) WILD-TYPE	126	65	103

Figure S434. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0016

Table S435. Gene #62: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 24(9P23) MUTATED	90	147	55
DEL PEAK 24(9P23) WILD-TYPE	80	126	98

Figure S435. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S436. Gene #62: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 24(9P23) MUTATED	87	63	36	66	40
DEL PEAK 24(9P23) WILD-TYPE	44	53	62	55	90

Figure S436. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.0065

Table S437. Gene #62: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 24(9P23) MUTATED	97	133	69
DEL PEAK 24(9P23) WILD-TYPE	70	145	103

Figure S437. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S438. Gene #62: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 24(9P23) MUTATED	83	72	61	54	29
DEL PEAK 24(9P23) WILD-TYPE	44	71	103	40	60

Figure S438. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.043

Table S439. Gene #62: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 24(9P23) MUTATED	74	79	57	22	27
DEL PEAK 24(9P23) WILD-TYPE	49	76	64	25	46

Figure S439. Get High-res Image Gene #62: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.043

Table S440. Gene #62: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 24(9P23) MUTATED	31	66	62	46	54
DEL PEAK 24(9P23) WILD-TYPE	20	58	82	62	38

Figure S440. Get High-res Image Gene #62: '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 = 2.8e-05

Table S441. Gene #63: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 25(9P21.3) MUTATED	94	76	147	17
DEL PEAK 25(9P21.3) WILD-TYPE	57	22	35	177

Figure S441. Get High-res Image Gene #63: '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 = 2.8e-05

Table S442. Gene #63: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 25(9P21.3) MUTATED	118	125	73
DEL PEAK 25(9P21.3) WILD-TYPE	123	36	102

Figure S442. Get High-res Image Gene #63: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S443. Gene #63: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 25(9P21.3) MUTATED	123	147	55
DEL PEAK 25(9P21.3) WILD-TYPE	47	126	98

Figure S443. Get High-res Image Gene #63: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S444. Gene #63: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 25(9P21.3) MUTATED	94	66	35	97	33
DEL PEAK 25(9P21.3) WILD-TYPE	37	50	63	24	97

Figure S444. Get High-res Image Gene #63: '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 = 2.8e-05

Table S445. Gene #63: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 25(9P21.3) MUTATED	121	134	76
DEL PEAK 25(9P21.3) WILD-TYPE	46	144	96

Figure S445. Get High-res Image Gene #63: '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 = 2.8e-05

Table S446. Gene #63: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 25(9P21.3) MUTATED	87	75	60	80	29
DEL PEAK 25(9P21.3) WILD-TYPE	40	68	104	14	60

Figure S446. Get High-res Image Gene #63: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S447. Gene #63: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 25(9P21.3) MUTATED	97	81	63	27	25
DEL PEAK 25(9P21.3) WILD-TYPE	26	74	58	20	48

Figure S447. Get High-res Image Gene #63: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S448. Gene #63: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 25(9P21.3) MUTATED	35	70	60	48	80
DEL PEAK 25(9P21.3) WILD-TYPE	16	54	84	60	12

Figure S448. Get High-res Image Gene #63: '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 = 2.8e-05

Table S449. Gene #64: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 26(9Q21.11) MUTATED	50	46	76	3
DEL PEAK 26(9Q21.11) WILD-TYPE	101	52	106	191

Figure S449. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S450. Gene #64: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 26(9Q21.11) MUTATED	56	68	42
DEL PEAK 26(9Q21.11) WILD-TYPE	185	93	133

Figure S450. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00433 (Fisher's exact test), Q value = 0.0073

Table S451. Gene #64: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 26(9Q21.11) MUTATED	60	79	29
DEL PEAK 26(9Q21.11) WILD-TYPE	110	194	124

Figure S451. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S452. Gene #64: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 26(9Q21.11) MUTATED	61	32	15	41	19
DEL PEAK 26(9Q21.11) WILD-TYPE	70	84	83	80	111

Figure S452. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S453. Gene #64: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 26(9Q21.11) MUTATED	68	63	42
DEL PEAK 26(9Q21.11) WILD-TYPE	99	215	130

Figure S453. Get High-res Image Gene #64: '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 = 2.8e-05

Table S454. Gene #64: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 26(9Q21.11) MUTATED	61	30	29	36	17
DEL PEAK 26(9Q21.11) WILD-TYPE	66	113	135	58	72

Figure S454. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.00085

Table S455. Gene #64: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 26(9Q21.11) MUTATED	53	38	34	15	11
DEL PEAK 26(9Q21.11) WILD-TYPE	70	117	87	32	62

Figure S455. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00082

Table S456. Gene #64: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 26(9Q21.11) MUTATED	25	30	30	30	36
DEL PEAK 26(9Q21.11) WILD-TYPE	26	94	114	78	56

Figure S456. Get High-res Image Gene #64: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S457. Gene #65: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 27(10P15.3) MUTATED	30	13	80	8
DEL PEAK 27(10P15.3) WILD-TYPE	121	85	102	186

Figure S457. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S458. Gene #65: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 27(10P15.3) MUTATED	46	52	24
DEL PEAK 27(10P15.3) WILD-TYPE	195	109	151

Figure S458. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 0.00406 (Fisher's exact test), Q value = 0.0069

Table S459. Gene #65: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 27(10P15.3) MUTATED	51	52	24
DEL PEAK 27(10P15.3) WILD-TYPE	119	221	129

Figure S459. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S460. Gene #65: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 27(10P15.3) MUTATED	33	23	18	42	11
DEL PEAK 27(10P15.3) WILD-TYPE	98	93	80	79	119

Figure S460. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.026

Table S461. Gene #65: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 27(10P15.3) MUTATED	47	56	27
DEL PEAK 27(10P15.3) WILD-TYPE	120	222	145

Figure S461. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S462. Gene #65: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 27(10P15.3) MUTATED	31	31	25	36	7
DEL PEAK 27(10P15.3) WILD-TYPE	96	112	139	58	82

Figure S462. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00176 (Fisher's exact test), Q value = 0.0032

Table S463. Gene #65: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 27(10P15.3) MUTATED	41	31	22	10	7
DEL PEAK 27(10P15.3) WILD-TYPE	82	124	99	37	66

Figure S463. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S464. Gene #65: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 27(10P15.3) MUTATED	15	24	20	16	36
DEL PEAK 27(10P15.3) WILD-TYPE	36	100	124	92	56

Figure S464. Get High-res Image Gene #65: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S465. Gene #66: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 28(10P11.21) MUTATED	19	11	69	3
DEL PEAK 28(10P11.21) WILD-TYPE	132	87	113	191

Figure S465. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S466. Gene #66: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 28(10P11.21) MUTATED	23	54	20
DEL PEAK 28(10P11.21) WILD-TYPE	218	107	155

Figure S466. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S467. Gene #66: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 28(10P11.21) MUTATED	51	30	17
DEL PEAK 28(10P11.21) WILD-TYPE	119	243	136

Figure S467. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S468. Gene #66: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 28(10P11.21) MUTATED	27	11	10	43	7
DEL PEAK 28(10P11.21) WILD-TYPE	104	105	88	78	123

Figure S468. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00019

Table S469. Gene #66: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 28(10P11.21) MUTATED	45	37	18
DEL PEAK 28(10P11.21) WILD-TYPE	122	241	154

Figure S469. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S470. Gene #66: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 28(10P11.21) MUTATED	25	18	14	40	3
DEL PEAK 28(10P11.21) WILD-TYPE	102	125	150	54	86

Figure S470. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S471. Gene #66: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 28(10P11.21) MUTATED	40	19	15	9	5
DEL PEAK 28(10P11.21) WILD-TYPE	83	136	106	38	68

Figure S471. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S472. Gene #66: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 28(10P11.21) MUTATED	10	13	14	11	40
DEL PEAK 28(10P11.21) WILD-TYPE	41	111	130	97	52

Figure S472. Get High-res Image Gene #66: 'del_10p11.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S473. Gene #67: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 29(10Q22.3) MUTATED	45	11	75	4
DEL PEAK 29(10Q22.3) WILD-TYPE	106	87	107	190

Figure S473. Get High-res Image Gene #67: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S474. Gene #67: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 29(10Q22.3) MUTATED	46	57	23
DEL PEAK 29(10Q22.3) WILD-TYPE	195	104	152

Figure S474. Get High-res Image Gene #67: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S475. Gene #67: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 29(10Q22.3) MUTATED	48	67	16
DEL PEAK 29(10Q22.3) WILD-TYPE	122	206	137

Figure S475. Get High-res Image Gene #67: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S476. Gene #67: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 29(10Q22.3) MUTATED	37	19	23	43	9
DEL PEAK 29(10Q22.3) WILD-TYPE	94	97	75	78	121

Figure S476. Get High-res Image Gene #67: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00049

Table S477. Gene #67: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 29(10Q22.3) MUTATED	50	63	21
DEL PEAK 29(10Q22.3) WILD-TYPE	117	215	151

Figure S477. Get High-res Image Gene #67: '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 = 2.8e-05

Table S478. Gene #67: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 29(10Q22.3) MUTATED	40	37	16	36	5
DEL PEAK 29(10Q22.3) WILD-TYPE	87	106	148	58	84

Figure S478. Get High-res Image Gene #67: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0021

Table S479. Gene #67: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 29(10Q22.3) MUTATED	43	30	20	9	9
DEL PEAK 29(10Q22.3) WILD-TYPE	80	125	101	38	64

Figure S479. Get High-res Image Gene #67: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S480. Gene #67: 'del_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 29(10Q22.3) MUTATED	15	32	14	14	36
DEL PEAK 29(10Q22.3) WILD-TYPE	36	92	130	94	56

Figure S480. Get High-res Image Gene #67: '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 = 2.8e-05

Table S481. Gene #68: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 30(10Q23.31) MUTATED	54	26	93	10
DEL PEAK 30(10Q23.31) WILD-TYPE	97	72	89	184

Figure S481. Get High-res Image Gene #68: '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 = 2.8e-05

Table S482. Gene #68: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 30(10Q23.31) MUTATED	63	72	34
DEL PEAK 30(10Q23.31) WILD-TYPE	178	89	141

Figure S482. Get High-res Image Gene #68: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 0.00765 (Fisher's exact test), Q value = 0.012

Table S483. Gene #68: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
DEL PEAK 30(10Q23.31) MUTATED	53	37	28	25
DEL PEAK 30(10Q23.31) WILD-TYPE	92	100	108	39

Figure S483. Get High-res Image Gene #68: 'del_10q23.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S484. Gene #68: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 30(10Q23.31) MUTATED	61	92	22
DEL PEAK 30(10Q23.31) WILD-TYPE	109	181	131

Figure S484. Get High-res Image Gene #68: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S485. Gene #68: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 30(10Q23.31) MUTATED	56	30	29	46	14
DEL PEAK 30(10Q23.31) WILD-TYPE	75	86	69	75	116

Figure S485. Get High-res Image Gene #68: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S486. Gene #68: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 30(10Q23.31) MUTATED	62	89	30
DEL PEAK 30(10Q23.31) WILD-TYPE	105	189	142

Figure S486. Get High-res Image Gene #68: '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 = 2.8e-05

Table S487. Gene #68: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 30(10Q23.31) MUTATED	56	45	31	40	9
DEL PEAK 30(10Q23.31) WILD-TYPE	71	98	133	54	80

Figure S487. Get High-res Image Gene #68: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.0032

Table S488. Gene #68: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 30(10Q23.31) MUTATED	52	48	26	13	14
DEL PEAK 30(10Q23.31) WILD-TYPE	71	107	95	34	59

Figure S488. Get High-res Image Gene #68: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S489. Gene #68: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 30(10Q23.31) MUTATED	22	42	29	20	40
DEL PEAK 30(10Q23.31) WILD-TYPE	29	82	115	88	52

Figure S489. Get High-res Image Gene #68: '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 = 2.8e-05

Table S490. Gene #69: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 31(11P15.5) MUTATED	51	32	81	11
DEL PEAK 31(11P15.5) WILD-TYPE	100	66	101	183

Figure S490. Get High-res Image Gene #69: '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 = 2.8e-05

Table S491. Gene #69: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 31(11P15.5) MUTATED	63	70	28
DEL PEAK 31(11P15.5) WILD-TYPE	178	91	147

Figure S491. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.021

Table S492. Gene #69: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
DEL PEAK 31(11P15.5) MUTATED	52	31	30	23
DEL PEAK 31(11P15.5) WILD-TYPE	93	106	106	41

Figure S492. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00522 (Fisher's exact test), Q value = 0.0087

Table S493. Gene #69: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 31(11P15.5) MUTATED	93	23	20
DEL PEAK 31(11P15.5) WILD-TYPE	180	87	79

Figure S493. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S494. Gene #69: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 31(11P15.5) MUTATED	70	71	24
DEL PEAK 31(11P15.5) WILD-TYPE	100	202	129

Figure S494. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S495. Gene #69: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 31(11P15.5) MUTATED	54	29	14	52	16
DEL PEAK 31(11P15.5) WILD-TYPE	77	87	84	69	114

Figure S495. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S496. Gene #69: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 31(11P15.5) MUTATED	72	64	36
DEL PEAK 31(11P15.5) WILD-TYPE	95	214	136

Figure S496. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S497. Gene #69: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 31(11P15.5) MUTATED	46	41	29	43	13
DEL PEAK 31(11P15.5) WILD-TYPE	81	102	135	51	76

Figure S497. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0023

Table S498. Gene #69: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 31(11P15.5) MUTATED	52	40	23	14	17
DEL PEAK 31(11P15.5) WILD-TYPE	71	115	98	33	56

Figure S498. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 0.00089

Table S499. Gene #69: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 31(11P15.5) MUTATED	14	38	30	22	42
DEL PEAK 31(11P15.5) WILD-TYPE	37	86	114	86	50

Figure S499. Get High-res Image Gene #69: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S500. Gene #70: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 32(11Q25) MUTATED	46	31	91	10
DEL PEAK 32(11Q25) WILD-TYPE	105	67	91	184

Figure S500. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S501. Gene #70: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 32(11Q25) MUTATED	65	75	30
DEL PEAK 32(11Q25) WILD-TYPE	176	86	145

Figure S501. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S502. Gene #70: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 32(11Q25) MUTATED	67	77	26
DEL PEAK 32(11Q25) WILD-TYPE	103	196	127

Figure S502. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S503. Gene #70: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 32(11Q25) MUTATED	50	30	19	55	16
DEL PEAK 32(11Q25) WILD-TYPE	81	86	79	66	114

Figure S503. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S504. Gene #70: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 32(11Q25) MUTATED	73	66	37
DEL PEAK 32(11Q25) WILD-TYPE	94	212	135

Figure S504. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S505. Gene #70: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 32(11Q25) MUTATED	40	39	32	51	14
DEL PEAK 32(11Q25) WILD-TYPE	87	104	132	43	75

Figure S505. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S506. Gene #70: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 32(11Q25) MUTATED	60	41	32	8	14
DEL PEAK 32(11Q25) WILD-TYPE	63	114	89	39	59

Figure S506. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S507. Gene #70: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 32(11Q25) MUTATED	15	39	30	21	50
DEL PEAK 32(11Q25) WILD-TYPE	36	85	114	87	42

Figure S507. Get High-res Image Gene #70: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S508. Gene #71: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 33(12P13.1) MUTATED	60	20	27	6
DEL PEAK 33(12P13.1) WILD-TYPE	91	78	155	188

Figure S508. Get High-res Image Gene #71: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.0075 (Fisher's exact test), Q value = 0.012

Table S509. Gene #71: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 33(12P13.1) MUTATED	52	34	19
DEL PEAK 33(12P13.1) WILD-TYPE	189	127	156

Figure S509. Get High-res Image Gene #71: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S510. Gene #71: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 33(12P13.1) MUTATED	48	20	12	15	13
DEL PEAK 33(12P13.1) WILD-TYPE	83	96	86	106	117

Figure S510. Get High-res Image Gene #71: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S511. Gene #71: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 33(12P13.1) MUTATED	44	28	21	7	12
DEL PEAK 33(12P13.1) WILD-TYPE	83	115	143	87	77

Figure S511. Get High-res Image Gene #71: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S512. Gene #71: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 33(12P13.1) MUTATED	21	26	27	20	7
DEL PEAK 33(12P13.1) WILD-TYPE	30	98	117	88	85

Figure S512. Get High-res Image Gene #71: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S513. Gene #72: 'del_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 34(12Q23.1) MUTATED	42	18	45	5
DEL PEAK 34(12Q23.1) WILD-TYPE	109	80	137	189

Figure S513. Get High-res Image Gene #72: 'del_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0021

Table S514. Gene #72: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 34(12Q23.1) MUTATED	45	41	18
DEL PEAK 34(12Q23.1) WILD-TYPE	196	120	157

Figure S514. Get High-res Image Gene #72: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00068

Table S515. Gene #72: 'del_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 34(12Q23.1) MUTATED	40	52	12
DEL PEAK 34(12Q23.1) WILD-TYPE	130	221	141

Figure S515. Get High-res Image Gene #72: 'del_12q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S516. Gene #72: 'del_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 34(12Q23.1) MUTATED	37	21	12	28	6
DEL PEAK 34(12Q23.1) WILD-TYPE	94	95	86	93	124

Figure S516. Get High-res Image Gene #72: 'del_12q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 7e-04

Table S517. Gene #72: 'del_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 34(12Q23.1) MUTATED	33	31	16	20	8
DEL PEAK 34(12Q23.1) WILD-TYPE	94	112	148	74	81

Figure S517. Get High-res Image Gene #72: 'del_12q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.017

Table S518. Gene #72: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 34(12Q23.1) MUTATED	30	36	19	8	5
DEL PEAK 34(12Q23.1) WILD-TYPE	93	119	102	39	68

Figure S518. Get High-res Image Gene #72: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S519. Gene #73: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 35(13Q12.11) MUTATED	14	48	67	9
DEL PEAK 35(13Q12.11) WILD-TYPE	137	50	115	185

Figure S519. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S520. Gene #73: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 35(13Q12.11) MUTATED	48	60	23
DEL PEAK 35(13Q12.11) WILD-TYPE	193	101	152

Figure S520. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S521. Gene #73: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 35(13Q12.11) MUTATED	64	49	21
DEL PEAK 35(13Q12.11) WILD-TYPE	106	224	132

Figure S521. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S522. Gene #73: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 35(13Q12.11) MUTATED	34	24	11	52	13
DEL PEAK 35(13Q12.11) WILD-TYPE	97	92	87	69	117

Figure S522. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S523. Gene #73: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 35(13Q12.11) MUTATED	63	45	30
DEL PEAK 35(13Q12.11) WILD-TYPE	104	233	142

Figure S523. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S524. Gene #73: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 35(13Q12.11) MUTATED	30	25	24	50	9
DEL PEAK 35(13Q12.11) WILD-TYPE	97	118	140	44	80

Figure S524. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S525. Gene #73: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 35(13Q12.11) MUTATED	49	31	24	10	9
DEL PEAK 35(13Q12.11) WILD-TYPE	74	124	97	37	64

Figure S525. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S526. Gene #73: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 35(13Q12.11) MUTATED	8	28	24	14	49
DEL PEAK 35(13Q12.11) WILD-TYPE	43	96	120	94	43

Figure S526. Get High-res Image Gene #73: 'del_13q12.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S527. Gene #74: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 36(13Q21.31) MUTATED	4	47	65	10
DEL PEAK 36(13Q21.31) WILD-TYPE	147	51	117	184

Figure S527. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q21.31' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S528. Gene #74: 'del_13q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 36(13Q21.31) MUTATED	43	53	21
DEL PEAK 36(13Q21.31) WILD-TYPE	198	108	154

Figure S528. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S529. Gene #74: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 36(13Q21.31) MUTATED	58	46	18
DEL PEAK 36(13Q21.31) WILD-TYPE	112	227	135

Figure S529. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_13q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S530. Gene #74: 'del_13q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 36(13Q21.31) MUTATED	25	27	9	49	12
DEL PEAK 36(13Q21.31) WILD-TYPE	106	89	89	72	118

Figure S530. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_13q21.31' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00041

Table S531. Gene #74: 'del_13q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 36(13Q21.31) MUTATED	53	48	25
DEL PEAK 36(13Q21.31) WILD-TYPE	114	230	147

Figure S531. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_13q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S532. Gene #74: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 36(13Q21.31) MUTATED	27	21	28	44	6
DEL PEAK 36(13Q21.31) WILD-TYPE	100	122	136	50	83

Figure S532. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.0012

Table S533. Gene #74: 'del_13q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 36(13Q21.31) MUTATED	42	26	21	12	8
DEL PEAK 36(13Q21.31) WILD-TYPE	81	129	100	35	65

Figure S533. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_13q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S534. Gene #74: 'del_13q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 36(13Q21.31) MUTATED	6	28	21	11	43
DEL PEAK 36(13Q21.31) WILD-TYPE	45	96	123	97	49

Figure S534. Get High-res Image Gene #74: 'del_13q21.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S535. Gene #75: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 37(14Q23.3) MUTATED	71	54	49	13
DEL PEAK 37(14Q23.3) WILD-TYPE	80	44	133	181

Figure S535. Get High-res Image Gene #75: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.004

Table S536. Gene #75: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 37(14Q23.3) MUTATED	71	64	39
DEL PEAK 37(14Q23.3) WILD-TYPE	170	97	136

Figure S536. Get High-res Image Gene #75: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.038

Table S537. Gene #75: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 37(14Q23.3) MUTATED	44	96	37
DEL PEAK 37(14Q23.3) WILD-TYPE	126	177	116

Figure S537. Get High-res Image Gene #75: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S538. Gene #75: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 37(14Q23.3) MUTATED	69	42	18	23	25
DEL PEAK 37(14Q23.3) WILD-TYPE	62	74	80	98	105

Figure S538. Get High-res Image Gene #75: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S539. Gene #75: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 37(14Q23.3) MUTATED	69	44	34	19	17
DEL PEAK 37(14Q23.3) WILD-TYPE	58	99	130	75	72

Figure S539. Get High-res Image Gene #75: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S540. Gene #75: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 37(14Q23.3) MUTATED	30	45	37	23	19
DEL PEAK 37(14Q23.3) WILD-TYPE	21	79	107	85	73

Figure S540. Get High-res Image Gene #75: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S541. Gene #76: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 38(15Q11.2) MUTATED	68	38	70	7
DEL PEAK 38(15Q11.2) WILD-TYPE	83	60	112	187

Figure S541. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

P value = 0.00722 (Fisher's exact test), Q value = 0.012

Table S542. Gene #76: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 38(15Q11.2) MUTATED	73	61	39
DEL PEAK 38(15Q11.2) WILD-TYPE	168	100	136

Figure S542. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.043

Table S543. Gene #76: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
DEL PEAK 38(15Q11.2) MUTATED	54	34	30	18
DEL PEAK 38(15Q11.2) WILD-TYPE	91	103	106	46

Figure S543. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.044

Table S544. Gene #76: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 38(15Q11.2) MUTATED	90	25	21
DEL PEAK 38(15Q11.2) WILD-TYPE	183	85	78

Figure S544. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00276 (Fisher's exact test), Q value = 0.0048

Table S545. Gene #76: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 38(15Q11.2) MUTATED	51	96	30
DEL PEAK 38(15Q11.2) WILD-TYPE	119	177	123

Figure S545. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S546. Gene #76: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 38(15Q11.2) MUTATED	55	40	29	36	17
DEL PEAK 38(15Q11.2) WILD-TYPE	76	76	69	85	113

Figure S546. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.039

Table S547. Gene #76: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 38(15Q11.2) MUTATED	54	90	37
DEL PEAK 38(15Q11.2) WILD-TYPE	113	188	135

Figure S547. Get High-res Image Gene #76: '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 = 2.8e-05

Table S548. Gene #76: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 38(15Q11.2) MUTATED	59	46	34	29	13
DEL PEAK 38(15Q11.2) WILD-TYPE	68	97	130	65	76

Figure S548. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.057

Table S549. Gene #76: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 38(15Q11.2) MUTATED	43	57	29	9	19
DEL PEAK 38(15Q11.2) WILD-TYPE	80	98	92	38	54

Figure S549. Get High-res Image Gene #76: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S550. Gene #77: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 39(16P13.3) MUTATED	84	38	47	8
DEL PEAK 39(16P13.3) WILD-TYPE	67	60	135	186

Figure S550. Get High-res Image Gene #77: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0012

Table S551. Gene #77: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 39(16P13.3) MUTATED	73	60	33
DEL PEAK 39(16P13.3) WILD-TYPE	168	101	142

Figure S551. Get High-res Image Gene #77: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S552. Gene #77: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 39(16P13.3) MUTATED	60	86	24
DEL PEAK 39(16P13.3) WILD-TYPE	110	187	129

Figure S552. Get High-res Image Gene #77: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S553. Gene #77: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 39(16P13.3) MUTATED	70	34	19	31	16
DEL PEAK 39(16P13.3) WILD-TYPE	61	82	79	90	114

Figure S553. Get High-res Image Gene #77: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0011

Table S554. Gene #77: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 39(16P13.3) MUTATED	63	79	33
DEL PEAK 39(16P13.3) WILD-TYPE	104	199	139

Figure S554. Get High-res Image Gene #77: '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 = 2.8e-05

Table S555. Gene #77: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 39(16P13.3) MUTATED	65	56	25	18	11
DEL PEAK 39(16P13.3) WILD-TYPE	62	87	139	76	78

Figure S555. Get High-res Image Gene #77: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S556. Gene #77: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 39(16P13.3) MUTATED	50	54	21	16	11
DEL PEAK 39(16P13.3) WILD-TYPE	73	101	100	31	62

Figure S556. Get High-res Image Gene #77: '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 = 2.8e-05

Table S557. Gene #77: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 39(16P13.3) MUTATED	32	46	32	24	18
DEL PEAK 39(16P13.3) WILD-TYPE	19	78	112	84	74

Figure S557. Get High-res Image Gene #77: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S558. Gene #78: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 40(16P13.3) MUTATED	71	36	41	5
DEL PEAK 40(16P13.3) WILD-TYPE	80	62	141	189

Figure S558. Get High-res Image Gene #78: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00107 (Fisher's exact test), Q value = 0.002

Table S559. Gene #78: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 40(16P13.3) MUTATED	60	55	29
DEL PEAK 40(16P13.3) WILD-TYPE	181	106	146

Figure S559. Get High-res Image Gene #78: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00262 (Fisher's exact test), Q value = 0.0046

Table S560. Gene #78: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 40(16P13.3) MUTATED	49	74	22
DEL PEAK 40(16P13.3) WILD-TYPE	121	199	131

Figure S560. Get High-res Image Gene #78: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S561. Gene #78: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 40(16P13.3) MUTATED	65	30	14	23	13
DEL PEAK 40(16P13.3) WILD-TYPE	66	86	84	98	117

Figure S561. Get High-res Image Gene #78: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S562. Gene #78: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 40(16P13.3) MUTATED	59	64	28
DEL PEAK 40(16P13.3) WILD-TYPE	108	214	144

Figure S562. Get High-res Image Gene #78: '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 = 2.8e-05

Table S563. Gene #78: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 40(16P13.3) MUTATED	63	45	17	15	11
DEL PEAK 40(16P13.3) WILD-TYPE	64	98	147	79	78

Figure S563. Get High-res Image Gene #78: '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 = 2.8e-05

Table S564. Gene #78: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 40(16P13.3) MUTATED	47	46	18	13	7
DEL PEAK 40(16P13.3) WILD-TYPE	76	109	103	34	66

Figure S564. Get High-res Image Gene #78: '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 = 2.8e-05

Table S565. Gene #78: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 40(16P13.3) MUTATED	30	41	24	21	15
DEL PEAK 40(16P13.3) WILD-TYPE	21	83	120	87	77

Figure S565. Get High-res Image Gene #78: '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 = 2.8e-05

Table S566. Gene #79: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 41(16Q23.1) MUTATED	99	60	68	38
DEL PEAK 41(16Q23.1) WILD-TYPE	52	38	114	156

Figure S566. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0013

Table S567. Gene #79: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 41(16Q23.1) MUTATED	121	69	55
DEL PEAK 41(16Q23.1) WILD-TYPE	120	92	120

Figure S567. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.055

Table S568. Gene #79: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 41(16Q23.1) MUTATED	70	129	53
DEL PEAK 41(16Q23.1) WILD-TYPE	100	144	100

Figure S568. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S569. Gene #79: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 41(16Q23.1) MUTATED	80	54	35	37	46
DEL PEAK 41(16Q23.1) WILD-TYPE	51	62	63	84	84

Figure S569. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.018

Table S570. Gene #79: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 41(16Q23.1) MUTATED	72	132	57
DEL PEAK 41(16Q23.1) WILD-TYPE	95	146	115

Figure S570. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S571. Gene #79: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 41(16Q23.1) MUTATED	73	75	65	21	27
DEL PEAK 41(16Q23.1) WILD-TYPE	54	68	99	73	62

Figure S571. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.0054

Table S572. Gene #79: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 41(16Q23.1) MUTATED	52	81	38	23	24
DEL PEAK 41(16Q23.1) WILD-TYPE	71	74	83	24	49

Figure S572. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S573. Gene #79: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 41(16Q23.1) MUTATED	34	66	57	40	21
DEL PEAK 41(16Q23.1) WILD-TYPE	17	58	87	68	71

Figure S573. Get High-res Image Gene #79: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S574. Gene #80: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 42(17P12) MUTATED	103	66	88	10
DEL PEAK 42(17P12) WILD-TYPE	48	32	94	184

Figure S574. Get High-res Image Gene #80: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S575. Gene #80: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 42(17P12) MUTATED	120	85	46
DEL PEAK 42(17P12) WILD-TYPE	121	76	129

Figure S575. Get High-res Image Gene #80: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S576. Gene #80: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 42(17P12) MUTATED	72	137	45
DEL PEAK 42(17P12) WILD-TYPE	98	136	108

Figure S576. Get High-res Image Gene #80: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S577. Gene #80: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 42(17P12) MUTATED	90	59	38	43	24
DEL PEAK 42(17P12) WILD-TYPE	41	57	60	78	106

Figure S577. Get High-res Image Gene #80: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S578. Gene #80: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 42(17P12) MUTATED	79	134	49
DEL PEAK 42(17P12) WILD-TYPE	88	144	123

Figure S578. Get High-res Image Gene #80: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S579. Gene #80: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 42(17P12) MUTATED	87	74	55	27	19
DEL PEAK 42(17P12) WILD-TYPE	40	69	109	67	70

Figure S579. Get High-res Image Gene #80: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.027

Table S580. Gene #80: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 42(17P12) MUTATED	58	81	42	16	28
DEL PEAK 42(17P12) WILD-TYPE	65	74	79	31	45

Figure S580. Get High-res Image Gene #80: '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 = 2.8e-05

Table S581. Gene #80: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 42(17P12) MUTATED	36	70	56	35	28
DEL PEAK 42(17P12) WILD-TYPE	15	54	88	73	64

Figure S581. Get High-res Image Gene #80: '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 = 2.8e-05

Table S582. Gene #81: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 43(17Q24.3) MUTATED	44	26	24	9
DEL PEAK 43(17Q24.3) WILD-TYPE	107	72	158	185

Figure S582. Get High-res Image Gene #81: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.018

Table S583. Gene #81: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 43(17Q24.3) MUTATED	44	31	16
DEL PEAK 43(17Q24.3) WILD-TYPE	197	130	159

Figure S583. Get High-res Image Gene #81: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S584. Gene #81: 'del_17q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 43(17Q24.3) MUTATED	36	15	23	15	10
DEL PEAK 43(17Q24.3) WILD-TYPE	95	101	75	106	120

Figure S584. Get High-res Image Gene #81: 'del_17q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.047

Table S585. Gene #81: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 43(17Q24.3) MUTATED	30	27	17	15	12
DEL PEAK 43(17Q24.3) WILD-TYPE	97	116	147	79	77

Figure S585. Get High-res Image Gene #81: '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 = 2.8e-05

Table S586. Gene #82: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 44(18Q12.2) MUTATED	92	59	115	26
DEL PEAK 44(18Q12.2) WILD-TYPE	59	39	67	168

Figure S586. Get High-res Image Gene #82: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.002

Table S587. Gene #82: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 44(18Q12.2) MUTATED	117	90	63
DEL PEAK 44(18Q12.2) WILD-TYPE	124	71	112

Figure S587. Get High-res Image Gene #82: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 0.00438 (Fisher's exact test), Q value = 0.0074

Table S588. Gene #82: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 44(18Q12.2) MUTATED	90	136	55
DEL PEAK 44(18Q12.2) WILD-TYPE	80	137	98

Figure S588. Get High-res Image Gene #82: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S589. Gene #82: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 44(18Q12.2) MUTATED	82	52	36	64	47
DEL PEAK 44(18Q12.2) WILD-TYPE	49	64	62	57	83

Figure S589. Get High-res Image Gene #82: 'del_18q12.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00051

Table S590. Gene #82: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 44(18Q12.2) MUTATED	76	69	63	51	30
DEL PEAK 44(18Q12.2) WILD-TYPE	51	74	101	43	59

Figure S590. Get High-res Image Gene #82: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00773 (Fisher's exact test), Q value = 0.012

Table S591. Gene #82: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 44(18Q12.2) MUTATED	62	83	54	24	21
DEL PEAK 44(18Q12.2) WILD-TYPE	61	72	67	23	52

Figure S591. Get High-res Image Gene #82: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.0095

Table S592. Gene #82: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 44(18Q12.2) MUTATED	32	62	62	38	50
DEL PEAK 44(18Q12.2) WILD-TYPE	19	62	82	70	42

Figure S592. Get High-res Image Gene #82: '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 = 2.8e-05

Table S593. Gene #83: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 45(18Q21.2) MUTATED	98	67	127	31
DEL PEAK 45(18Q21.2) WILD-TYPE	53	31	55	163

Figure S593. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S594. Gene #83: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 45(18Q21.2) MUTATED	137	96	68
DEL PEAK 45(18Q21.2) WILD-TYPE	104	65	107

Figure S594. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.0022

Table S595. Gene #83: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 45(18Q21.2) MUTATED	98	153	60
DEL PEAK 45(18Q21.2) WILD-TYPE	72	120	93

Figure S595. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.0011

Table S596. Gene #83: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 45(18Q21.2) MUTATED	86	60	45	68	52
DEL PEAK 45(18Q21.2) WILD-TYPE	45	56	53	53	78

Figure S596. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.068

Table S597. Gene #83: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 45(18Q21.2) MUTATED	95	149	76
DEL PEAK 45(18Q21.2) WILD-TYPE	72	129	96

Figure S597. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S598. Gene #83: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 45(18Q21.2) MUTATED	82	83	69	54	32
DEL PEAK 45(18Q21.2) WILD-TYPE	45	60	95	40	57

Figure S598. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00843 (Fisher's exact test), Q value = 0.013

Table S599. Gene #83: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 45(18Q21.2) MUTATED	66	91	59	28	25
DEL PEAK 45(18Q21.2) WILD-TYPE	57	64	62	19	48

Figure S599. Get High-res Image Gene #83: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00914 (Fisher's exact test), Q value = 0.015

Table S600. Gene #83: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 45(18Q21.2) MUTATED	32	73	68	43	53
DEL PEAK 45(18Q21.2) WILD-TYPE	19	51	76	65	39

Figure S600. Get High-res Image Gene #83: '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 = 2.8e-05

Table S601. Gene #84: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 46(19P13.3) MUTATED	92	51	97	9
DEL PEAK 46(19P13.3) WILD-TYPE	59	47	85	185

Figure S601. Get High-res Image Gene #84: '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 = 2.8e-05

Table S602. Gene #84: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 46(19P13.3) MUTATED	91	99	43
DEL PEAK 46(19P13.3) WILD-TYPE	150	62	132

Figure S602. Get High-res Image Gene #84: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.0061

Table S603. Gene #84: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	145	137	136	64
DEL PEAK 46(19P13.3) MUTATED	70	49	39	30
DEL PEAK 46(19P13.3) WILD-TYPE	75	88	97	34

Figure S603. Get High-res Image Gene #84: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00083 (Fisher's exact test), Q value = 0.0016

Table S604. Gene #84: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	273	110	99
DEL PEAK 46(19P13.3) MUTATED	126	35	27
DEL PEAK 46(19P13.3) WILD-TYPE	147	75	72

Figure S604. Get High-res Image Gene #84: '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 = 2.8e-05

Table S605. Gene #84: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 46(19P13.3) MUTATED	85	125	31
DEL PEAK 46(19P13.3) WILD-TYPE	85	148	122

Figure S605. Get High-res Image Gene #84: '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 = 2.8e-05

Table S606. Gene #84: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 46(19P13.3) MUTATED	98	47	27	54	15
DEL PEAK 46(19P13.3) WILD-TYPE	33	69	71	67	115

Figure S606. Get High-res Image Gene #84: '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 = 2.8e-05

Table S607. Gene #84: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 46(19P13.3) MUTATED	98	110	38
DEL PEAK 46(19P13.3) WILD-TYPE	69	168	134

Figure S607. Get High-res Image Gene #84: '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 = 2.8e-05

Table S608. Gene #84: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 46(19P13.3) MUTATED	100	62	32	43	9
DEL PEAK 46(19P13.3) WILD-TYPE	27	81	132	51	80

Figure S608. Get High-res Image Gene #84: '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 = 2.8e-05

Table S609. Gene #84: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 46(19P13.3) MUTATED	75	71	28	17	21
DEL PEAK 46(19P13.3) WILD-TYPE	48	84	93	30	52

Figure S609. Get High-res Image Gene #84: '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 = 2.8e-05

Table S610. Gene #84: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 46(19P13.3) MUTATED	40	65	35	30	42
DEL PEAK 46(19P13.3) WILD-TYPE	11	59	109	78	50

Figure S610. Get High-res Image Gene #84: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S611. Gene #85: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 47(20P12.1) MUTATED	14	26	23	9
DEL PEAK 47(20P12.1) WILD-TYPE	137	72	159	185

Figure S611. Get High-res Image Gene #85: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.025

Table S612. Gene #85: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 47(20P12.1) MUTATED	26	36	9
DEL PEAK 47(20P12.1) WILD-TYPE	144	237	144

Figure S612. Get High-res Image Gene #85: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.0016

Table S613. Gene #85: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 47(20P12.1) MUTATED	23	21	8	14	5
DEL PEAK 47(20P12.1) WILD-TYPE	108	95	90	107	125

Figure S613. Get High-res Image Gene #85: 'del_20p12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.0043

Table S614. Gene #85: 'del_20p12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 47(20P12.1) MUTATED	27	13	16	12	4
DEL PEAK 47(20P12.1) WILD-TYPE	100	130	148	82	85

Figure S614. Get High-res Image Gene #85: '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 = 2.8e-05

Table S615. Gene #86: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 48(21Q11.2) MUTATED	99	59	103	25
DEL PEAK 48(21Q11.2) WILD-TYPE	52	39	79	169

Figure S615. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0053

Table S616. Gene #86: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 48(21Q11.2) MUTATED	120	87	64
DEL PEAK 48(21Q11.2) WILD-TYPE	121	74	111

Figure S616. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00047

Table S617. Gene #86: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 48(21Q11.2) MUTATED	93	131	50
DEL PEAK 48(21Q11.2) WILD-TYPE	77	142	103

Figure S617. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S618. Gene #86: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 48(21Q11.2) MUTATED	80	52	38	68	36
DEL PEAK 48(21Q11.2) WILD-TYPE	51	64	60	53	94

Figure S618. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.043

Table S619. Gene #86: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 48(21Q11.2) MUTATED	88	129	66
DEL PEAK 48(21Q11.2) WILD-TYPE	79	149	106

Figure S619. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S620. Gene #86: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 48(21Q11.2) MUTATED	77	75	54	49	28
DEL PEAK 48(21Q11.2) WILD-TYPE	50	68	110	45	61

Figure S620. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00368 (Fisher's exact test), Q value = 0.0063

Table S621. Gene #86: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 48(21Q11.2) MUTATED	68	81	47	26	24
DEL PEAK 48(21Q11.2) WILD-TYPE	55	74	74	21	49

Figure S621. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00671 (Fisher's exact test), Q value = 0.011

Table S622. Gene #86: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 48(21Q11.2) MUTATED	31	68	54	45	48
DEL PEAK 48(21Q11.2) WILD-TYPE	20	56	90	63	44

Figure S622. Get High-res Image Gene #86: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S623. Gene #87: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 49(21Q22.13) MUTATED	105	63	110	27
DEL PEAK 49(21Q22.13) WILD-TYPE	46	35	72	167

Figure S623. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'METHLYATION_CNMF'

P value = 0.00551 (Fisher's exact test), Q value = 0.0092

Table S624. Gene #87: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 49(21Q22.13) MUTATED	131	86	69
DEL PEAK 49(21Q22.13) WILD-TYPE	110	75	106

Figure S624. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.13' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00033

Table S625. Gene #87: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 49(21Q22.13) MUTATED	98	141	54
DEL PEAK 49(21Q22.13) WILD-TYPE	72	132	99

Figure S625. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S626. Gene #87: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 49(21Q22.13) MUTATED	82	61	39	72	39
DEL PEAK 49(21Q22.13) WILD-TYPE	49	55	59	49	91

Figure S626. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.012

Table S627. Gene #87: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 49(21Q22.13) MUTATED	91	144	67
DEL PEAK 49(21Q22.13) WILD-TYPE	76	134	105

Figure S627. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S628. Gene #87: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 49(21Q22.13) MUTATED	79	81	61	52	29
DEL PEAK 49(21Q22.13) WILD-TYPE	48	62	103	42	60

Figure S628. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00039

Table S629. Gene #87: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 49(21Q22.13) MUTATED	71	87	46	31	26
DEL PEAK 49(21Q22.13) WILD-TYPE	52	68	75	16	47

Figure S629. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.023

Table S630. Gene #87: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 49(21Q22.13) MUTATED	30	73	62	45	51
DEL PEAK 49(21Q22.13) WILD-TYPE	21	51	82	63	41

Figure S630. Get High-res Image Gene #87: 'del_21q22.13' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S631. Gene #88: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 50(22Q11.1) MUTATED	92	65	65	8
DEL PEAK 50(22Q11.1) WILD-TYPE	59	33	117	186

Figure S631. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.0056

Table S632. Gene #88: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 50(22Q11.1) MUTATED	98	68	47
DEL PEAK 50(22Q11.1) WILD-TYPE	143	93	128

Figure S632. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MRNASEQ_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0053

Table S633. Gene #88: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 50(22Q11.1) MUTATED	62	118	41
DEL PEAK 50(22Q11.1) WILD-TYPE	108	155	112

Figure S633. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S634. Gene #88: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 50(22Q11.1) MUTATED	72	50	33	37	29
DEL PEAK 50(22Q11.1) WILD-TYPE	59	66	65	84	101

Figure S634. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 0.00477 (Fisher's exact test), Q value = 0.008

Table S635. Gene #88: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 50(22Q11.1) MUTATED	69	112	46
DEL PEAK 50(22Q11.1) WILD-TYPE	98	166	126

Figure S635. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S636. Gene #88: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 50(22Q11.1) MUTATED	76	72	34	25	20
DEL PEAK 50(22Q11.1) WILD-TYPE	51	71	130	69	69

Figure S636. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00363 (Fisher's exact test), Q value = 0.0062

Table S637. Gene #88: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 50(22Q11.1) MUTATED	47	72	32	20	20
DEL PEAK 50(22Q11.1) WILD-TYPE	76	83	89	27	53

Figure S637. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.9e-05

Table S638. Gene #88: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 50(22Q11.1) MUTATED	30	59	43	35	24
DEL PEAK 50(22Q11.1) WILD-TYPE	21	65	101	73	68

Figure S638. Get High-res Image Gene #88: 'del_22q11.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S639. Gene #89: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 51(22Q13.31) MUTATED	85	68	71	11
DEL PEAK 51(22Q13.31) WILD-TYPE	66	30	111	183

Figure S639. Get High-res Image Gene #89: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0014

Table S640. Gene #89: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 51(22Q13.31) MUTATED	100	72	46
DEL PEAK 51(22Q13.31) WILD-TYPE	141	89	129

Figure S640. Get High-res Image Gene #89: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.012

Table S641. Gene #89: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 51(22Q13.31) MUTATED	62	120	44
DEL PEAK 51(22Q13.31) WILD-TYPE	108	153	109

Figure S641. Get High-res Image Gene #89: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S642. Gene #89: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 51(22Q13.31) MUTATED	75	54	31	37	29
DEL PEAK 51(22Q13.31) WILD-TYPE	56	62	67	84	101

Figure S642. Get High-res Image Gene #89: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00093

Table S643. Gene #89: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 51(22Q13.31) MUTATED	70	118	44
DEL PEAK 51(22Q13.31) WILD-TYPE	97	160	128

Figure S643. Get High-res Image Gene #89: '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 = 2.8e-05

Table S644. Gene #89: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 51(22Q13.31) MUTATED	78	67	40	27	20
DEL PEAK 51(22Q13.31) WILD-TYPE	49	76	124	67	69

Figure S644. Get High-res Image Gene #89: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00233 (Fisher's exact test), Q value = 0.0042

Table S645. Gene #89: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 51(22Q13.31) MUTATED	50	75	31	20	25
DEL PEAK 51(22Q13.31) WILD-TYPE	73	80	90	27	48

Figure S645. Get High-res Image Gene #89: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S646. Gene #89: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 51(22Q13.31) MUTATED	33	60	48	34	26
DEL PEAK 51(22Q13.31) WILD-TYPE	18	64	96	74	66

Figure S646. Get High-res Image Gene #89: '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 = 2.8e-05

Table S647. Gene #90: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 52(XP22.2) MUTATED	38	32	70	11
DEL PEAK 52(XP22.2) WILD-TYPE	113	66	112	183

Figure S647. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S648. Gene #90: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 52(XP22.2) MUTATED	61	62	22
DEL PEAK 52(XP22.2) WILD-TYPE	180	99	153

Figure S648. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S649. Gene #90: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 52(XP22.2) MUTATED	62	60	23
DEL PEAK 52(XP22.2) WILD-TYPE	108	213	130

Figure S649. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0012

Table S650. Gene #90: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 52(XP22.2) MUTATED	38	23	24	43	17
DEL PEAK 52(XP22.2) WILD-TYPE	93	93	74	78	113

Figure S650. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S651. Gene #90: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 52(XP22.2) MUTATED	60	64	26
DEL PEAK 52(XP22.2) WILD-TYPE	107	214	146

Figure S651. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S652. Gene #90: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 52(XP22.2) MUTATED	44	30	24	40	12
DEL PEAK 52(XP22.2) WILD-TYPE	83	113	140	54	77

Figure S652. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.062

Table S653. Gene #90: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 52(XP22.2) MUTATED	46	38	25	11	18
DEL PEAK 52(XP22.2) WILD-TYPE	77	117	96	36	55

Figure S653. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00076

Table S654. Gene #90: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 52(XP22.2) MUTATED	17	32	26	23	40
DEL PEAK 52(XP22.2) WILD-TYPE	34	92	118	85	52

Figure S654. Get High-res Image Gene #90: 'del_xp22.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S655. Gene #91: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 53(XP21.1) MUTATED	41	27	71	7
DEL PEAK 53(XP21.1) WILD-TYPE	110	71	111	187

Figure S655. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S656. Gene #91: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 53(XP21.1) MUTATED	57	58	23
DEL PEAK 53(XP21.1) WILD-TYPE	184	103	152

Figure S656. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S657. Gene #91: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 53(XP21.1) MUTATED	66	54	20
DEL PEAK 53(XP21.1) WILD-TYPE	104	219	133

Figure S657. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S658. Gene #91: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 53(XP21.1) MUTATED	36	25	17	47	15
DEL PEAK 53(XP21.1) WILD-TYPE	95	91	81	74	115

Figure S658. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S659. Gene #91: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 53(XP21.1) MUTATED	61	59	23
DEL PEAK 53(XP21.1) WILD-TYPE	106	219	149

Figure S659. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S660. Gene #91: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 53(XP21.1) MUTATED	35	30	24	42	12
DEL PEAK 53(XP21.1) WILD-TYPE	92	113	140	52	77

Figure S660. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0012

Table S661. Gene #91: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 53(XP21.1) MUTATED	49	39	22	9	12
DEL PEAK 53(XP21.1) WILD-TYPE	74	116	99	38	61

Figure S661. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.6e-05

Table S662. Gene #91: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 53(XP21.1) MUTATED	16	29	25	19	42
DEL PEAK 53(XP21.1) WILD-TYPE	35	95	119	89	50

Figure S662. Get High-res Image Gene #91: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S663. Gene #92: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 54(XP11.3) MUTATED	39	31	72	6
DEL PEAK 54(XP11.3) WILD-TYPE	112	67	110	188

Figure S663. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S664. Gene #92: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 54(XP11.3) MUTATED	57	63	20
DEL PEAK 54(XP11.3) WILD-TYPE	184	98	155

Figure S664. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S665. Gene #92: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 54(XP11.3) MUTATED	69	56	17
DEL PEAK 54(XP11.3) WILD-TYPE	101	217	136

Figure S665. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S666. Gene #92: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 54(XP11.3) MUTATED	32	28	17	52	13
DEL PEAK 54(XP11.3) WILD-TYPE	99	88	81	69	117

Figure S666. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S667. Gene #92: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 54(XP11.3) MUTATED	61	61	24
DEL PEAK 54(XP11.3) WILD-TYPE	106	217	148

Figure S667. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S668. Gene #92: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 54(XP11.3) MUTATED	35	29	23	48	11
DEL PEAK 54(XP11.3) WILD-TYPE	92	114	141	46	78

Figure S668. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0017

Table S669. Gene #92: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	155	121	47	73
DEL PEAK 54(XP11.3) MUTATED	49	39	23	10	12
DEL PEAK 54(XP11.3) WILD-TYPE	74	116	98	37	61

Figure S669. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S670. Gene #92: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 54(XP11.3) MUTATED	13	32	21	19	48
DEL PEAK 54(XP11.3) WILD-TYPE	38	92	123	89	44

Figure S670. Get High-res Image Gene #92: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S671. Gene #93: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 55(XQ11.2) MUTATED	33	18	49	5
DEL PEAK 55(XQ11.2) WILD-TYPE	118	80	133	189

Figure S671. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq11.2' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00041

Table S672. Gene #93: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 55(XQ11.2) MUTATED	45	38	14
DEL PEAK 55(XQ11.2) WILD-TYPE	196	123	161

Figure S672. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq11.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00045

Table S673. Gene #93: 'del_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 55(XQ11.2) MUTATED	42	47	12
DEL PEAK 55(XQ11.2) WILD-TYPE	128	226	141

Figure S673. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.016

Table S674. Gene #93: 'del_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 55(XQ11.2) MUTATED	29	23	15	24	10
DEL PEAK 55(XQ11.2) WILD-TYPE	102	93	83	97	120

Figure S674. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_CNMF'

P value = 0.00166 (Fisher's exact test), Q value = 0.003

Table S675. Gene #93: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 55(XQ11.2) MUTATED	36	53	15
DEL PEAK 55(XQ11.2) WILD-TYPE	131	225	157

Figure S675. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00298 (Fisher's exact test), Q value = 0.0052

Table S676. Gene #93: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 55(XQ11.2) MUTATED	25	32	20	21	6
DEL PEAK 55(XQ11.2) WILD-TYPE	102	111	144	73	83

Figure S676. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.047

Table S677. Gene #93: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	51	124	144	108	92
DEL PEAK 55(XQ11.2) MUTATED	12	26	19	11	21
DEL PEAK 55(XQ11.2) WILD-TYPE	39	98	125	97	71

Figure S677. Get High-res Image Gene #93: 'del_xq11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S678. Gene #94: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	151	98	182	194
DEL PEAK 56(XQ21.33) MUTATED	39	19	34	6
DEL PEAK 56(XQ21.33) WILD-TYPE	112	79	148	188

Figure S678. Get High-res Image Gene #94: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S679. Gene #94: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	241	161	175
DEL PEAK 56(XQ21.33) MUTATED	39	39	12
DEL PEAK 56(XQ21.33) WILD-TYPE	202	122	163

Figure S679. Get High-res Image Gene #94: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00057

Table S680. Gene #94: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	170	273	153
DEL PEAK 56(XQ21.33) MUTATED	39	45	11
DEL PEAK 56(XQ21.33) WILD-TYPE	131	228	142

Figure S680. Get High-res Image Gene #94: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00565 (Fisher's exact test), Q value = 0.0094

Table S681. Gene #94: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	131	116	98	121	130
DEL PEAK 56(XQ21.33) MUTATED	30	21	14	21	9
DEL PEAK 56(XQ21.33) WILD-TYPE	101	95	84	100	121

Figure S681. Get High-res Image Gene #94: 'del_xq21.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.00839 (Fisher's exact test), Q value = 0.013

Table S682. Gene #94: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	167	278	172
DEL PEAK 56(XQ21.33) MUTATED	37	43	17
DEL PEAK 56(XQ21.33) WILD-TYPE	130	235	155

Figure S682. Get High-res Image Gene #94: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00033

Table S683. Gene #94: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	143	164	94	89
DEL PEAK 56(XQ21.33) MUTATED	29	30	15	18	5
DEL PEAK 56(XQ21.33) WILD-TYPE	98	113	149	76	84

Figure S683. Get High-res Image Gene #94: 'del_xq21.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STES-TP/22532764/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/22555833/STES-TP.transferedmergedcluster.txt
Number of patients = 625
Number of significantly focal cnvs = 94
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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