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 67 focal events and 12 molecular subtypes across 1079 patients, 644 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_1q44 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_3p25.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_3q26.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_6p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p15.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_11q14.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_12p13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q34 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
amp_17q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.42 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_1p22.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_6q15 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6q27 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', '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 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q23.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 67 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 644 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1p22 3	250 (23%)	829	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00027 (0.0545)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)
amp 3q26 32	340 (32%)	739	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	3e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 6p23	298 (28%)	781	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	4e-05 (0.0103)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 6q21	201 (19%)	878	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 8q24 21	677 (63%)	402	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 10p15 1	304 (28%)	775	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 12p13 33	281 (26%)	798	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 13q34	179 (17%)	900	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)
amp 19q12	283 (26%)	796	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00107 (0.179)
amp 20q13 2	547 (51%)	532	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00061 (0.113)	0.00021 (0.0439)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 2q37 3	316 (29%)	763	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	7e-05 (0.0169)
del 3p21 31	347 (32%)	732	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00014 (0.0305)
del 4p16 3	339 (31%)	740	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00027 (0.0545)
del 4q35 1	345 (32%)	734	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00071 (0.129)
del 5q11 2	280 (26%)	799	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 5q21 3	272 (25%)	807	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 9q34 2	296 (27%)	783	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 10q23 31	320 (30%)	759	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00011 (0.0249)
del 10q26 3	319 (30%)	760	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 11p15 5	309 (29%)	770	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)
del 12q23 1	201 (19%)	878	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 12q24 31	211 (20%)	868	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)	2e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.0001 (0.0228)
del 14q24 1	353 (33%)	726	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 15q13 1	374 (35%)	705	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	3e-05 (0.00804)	8e-05 (0.019)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 16q24 3	692 (64%)	387	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 17q21 31	371 (34%)	708	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00041 (0.0787)
del 19p13 3	363 (34%)	716	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 19q13 32	216 (20%)	863	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00058 (0.108)	3e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 20p13	160 (15%)	919	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00038 (0.0737)	0.00093 (0.159)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
amp 17q23 1	425 (39%)	654	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.361 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	8e-05 (0.019)	1e-05 (0.00804)
del 8p23 2	557 (52%)	522	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00856 (0.95)	0.00074 (0.134)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 9p23	324 (30%)	755	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.0102 (1.00)	0.00093 (0.159)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00024 (0.049)	8e-05 (0.019)
del 9q21 11	293 (27%)	786	0.00114 (0.188)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00777 (0.894)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)
del 13q14 2	494 (46%)	585	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.264 (1.00)	4e-05 (0.0103)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	3e-05 (0.00804)
amp 17q12	332 (31%)	747	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.095 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00451 (0.586)	1e-05 (0.00804)	0.0003 (0.0594)	0.00018 (0.038)
amp 19p13 12	229 (21%)	850	8e-05 (0.019)	0.00022 (0.0451)	1e-05 (0.00804)	8e-05 (0.019)	0.00091 (0.157)	0.00215 (0.333)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.0904 (1.00)
del 7p22 3	136 (13%)	943	4e-05 (0.0103)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00221 (0.336)	0.00491 (0.619)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)	5e-05 (0.0126)
del 9p21 3	363 (34%)	716	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00516 (0.635)	0.00443 (0.58)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	7e-05 (0.0169)	1e-05 (0.00804)
del 17p12	650 (60%)	429	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)	0.0581 (1.00)	0.149 (1.00)
amp 1q21 3	781 (72%)	298	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	3e-05 (0.00804)	0.0476 (1.00)	0.0128 (1.00)	0.00086 (0.151)	1e-05 (0.00804)	0.0005 (0.095)	1e-05 (0.00804)	0.00113 (0.188)	0.121 (1.00)
amp 4q13 3	163 (15%)	916	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	2e-05 (0.00804)	0.0673 (1.00)	0.0427 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00335 (0.472)	3e-05 (0.00804)
amp 12q15	275 (25%)	804	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00021 (0.0439)	0.29 (1.00)	0.00486 (0.617)	1e-05 (0.00804)	1e-05 (0.00804)	7e-05 (0.0169)	1e-05 (0.00804)	2e-05 (0.00804)	0.168 (1.00)
amp 15q26 3	194 (18%)	885	1e-05 (0.00804)	0.00011 (0.0249)	1e-05 (0.00804)	0.00117 (0.192)	0.00216 (0.333)	0.00719 (0.834)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00185 (0.292)	5e-05 (0.0126)
del 8p11 21	200 (19%)	879	6e-05 (0.0148)	0.00012 (0.0266)	1e-05 (0.00804)	0.00813 (0.919)	0.0198 (1.00)	0.00013 (0.0286)	2e-05 (0.00804)	1e-05 (0.00804)	4e-05 (0.0103)	1e-05 (0.00804)	0.00253 (0.372)	0.00052 (0.0983)
del 11q23 3	546 (51%)	533	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.92 (1.00)	3e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.0337 (1.00)	5e-05 (0.0126)	0.0002 (0.042)	0.175 (1.00)
amp 3p25 1	198 (18%)	881	0.0007 (0.128)	5e-05 (0.0126)	1e-05 (0.00804)	0.00021 (0.0439)	0.244 (1.00)	0.379 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.0389 (1.00)	0.07 (1.00)
amp 8p11 21	420 (39%)	659	0.0427 (1.00)	0.00463 (0.597)	1e-05 (0.00804)	5e-05 (0.0126)	0.9 (1.00)	0.0755 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	0.00148 (0.238)	2e-05 (0.00804)	6e-05 (0.0148)	0.00088 (0.154)
amp 11p13	222 (21%)	857	0.164 (1.00)	0.0009 (0.157)	1e-05 (0.00804)	0.00386 (0.533)	0.0608 (1.00)	0.0486 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00013 (0.0286)	0.00015 (0.0324)
amp 19q13 42	275 (25%)	804	0.0004 (0.0772)	0.00242 (0.361)	1e-05 (0.00804)	0.00092 (0.158)	0.00119 (0.194)	0.245 (1.00)	0.00021 (0.0439)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.177 (1.00)	0.0768 (1.00)
del 1p36 13	451 (42%)	628	6e-05 (0.0148)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00375 (0.521)	0.00414 (0.555)	1e-05 (0.00804)	1e-05 (0.00804)	0.00011 (0.0249)	2e-05 (0.00804)	0.00232 (0.35)	0.165 (1.00)
del 6q15	358 (33%)	721	1e-05 (0.00804)	0.00032 (0.0627)	1e-05 (0.00804)	1e-05 (0.00804)	0.456 (1.00)	0.0136 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	0.028 (1.00)	1e-05 (0.00804)	0.00014 (0.0305)	0.557 (1.00)
del 7q36 1	199 (18%)	880	0.00265 (0.384)	1e-05 (0.00804)	1e-05 (0.00804)	0.00217 (0.333)	0.311 (1.00)	0.0318 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	8e-05 (0.019)	2e-05 (0.00804)
del 18q23	354 (33%)	725	0.0001 (0.0228)	4e-05 (0.0103)	1e-05 (0.00804)	1e-05 (0.00804)	0.00403 (0.549)	0.0296 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.005 (0.625)	0.169 (1.00)
amp 5p15 33	393 (36%)	686	0.00847 (0.949)	0.00085 (0.15)	1e-05 (0.00804)	1e-05 (0.00804)	0.0465 (1.00)	0.474 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00167 (0.267)	0.00503 (0.625)
amp 8p11 23	411 (38%)	668	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00017 (0.036)	0.0533 (1.00)	8e-05 (0.019)	1e-05 (0.00804)	1e-05 (0.00804)	0.552 (1.00)	0.0924 (1.00)	0.179 (1.00)	0.742 (1.00)
amp 10q22 3	150 (14%)	929	7e-05 (0.0169)	6e-05 (0.0148)	1e-05 (0.00804)	0.00243 (0.361)	0.00464 (0.597)	0.486 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00181 (0.288)	0.00275 (0.393)
amp 11q13 3	397 (37%)	682	0.00016 (0.0342)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.983 (1.00)	0.0006 (0.112)	8e-05 (0.019)	1e-05 (0.00804)	0.00193 (0.303)	0.00569 (0.677)	0.0146 (1.00)	0.00791 (0.902)
amp 11q14 1	266 (25%)	813	0.00552 (0.662)	0.00012 (0.0266)	1e-05 (0.00804)	6e-05 (0.0148)	0.0822 (1.00)	0.257 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.00028 (0.0557)	0.0301 (1.00)	0.0194 (1.00)
amp 14q21 1	220 (20%)	859	2e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	8e-05 (0.019)	0.0716 (1.00)	0.00271 (0.39)	1e-05 (0.00804)	1e-05 (0.00804)	0.00667 (0.78)	1e-05 (0.00804)	0.00439 (0.579)	0.679 (1.00)
del 1p22 1	361 (33%)	718	0.0105 (1.00)	1e-05 (0.00804)	1e-05 (0.00804)	1e-05 (0.00804)	0.0162 (1.00)	0.00195 (0.304)	1e-05 (0.00804)	1e-05 (0.00804)	0.0451 (1.00)	1e-05 (0.00804)	0.202 (1.00)	0.967 (1.00)
amp 1q44	789 (73%)	290	3e-05 (0.00804)	0.00106 (0.178)	1e-05 (0.00804)	0.00403 (0.549)	0.854 (1.00)	0.361 (1.00)	0.894 (1.00)	0.00015 (0.0324)	0.758 (1.00)	0.00016 (0.0342)	0.113 (1.00)	0.139 (1.00)
del 21q11 2	217 (20%)	862	0.00024 (0.049)	0.00401 (0.549)	1e-05 (0.00804)	0.00027 (0.0545)	0.0614 (1.00)	0.00914 (1.00)	0.00031 (0.0611)	1e-05 (0.00804)	0.00531 (0.643)	0.00365 (0.511)	0.0332 (1.00)	0.124 (1.00)
del 12p13 1	188 (17%)	891	0.0341 (1.00)	0.111 (1.00)	0.00011 (0.0249)	0.0427 (1.00)	0.289 (1.00)	0.313 (1.00)	0.00083 (0.148)	0.00054 (0.102)	0.00236 (0.354)	9e-05 (0.0206)	0.00593 (0.7)	0.00283 (0.402)
del 22q13 32	492 (46%)	587	0.255 (1.00)	0.0097 (1.00)	1e-05 (0.00804)	0.0821 (1.00)	0.174 (1.00)	0.017 (1.00)	0.00143 (0.232)	0.00066 (0.121)	0.0308 (1.00)	0.00076 (0.136)	0.00258 (0.377)	0.0765 (1.00)
amp 17p11 2	146 (14%)	933	0.0273 (1.00)	0.0598 (1.00)	1e-05 (0.00804)	0.00074 (0.134)	0.712 (1.00)	0.0184 (1.00)	0.00045 (0.0859)	0.0137 (1.00)	0.667 (1.00)	0.102 (1.00)	0.603 (1.00)	0.1 (1.00)
del 6p25 3	204 (19%)	875	0.406 (1.00)	0.775 (1.00)	1e-05 (0.00804)	0.00414 (0.555)	0.306 (1.00)	0.0996 (1.00)	0.00032 (0.0627)	0.022 (1.00)	0.00521 (0.636)	0.00925 (1.00)	0.312 (1.00)	0.181 (1.00)
del 6q27	375 (35%)	704	0.0218 (1.00)	0.0108 (1.00)	1e-05 (0.00804)	0.15 (1.00)	0.0567 (1.00)	0.0628 (1.00)	0.0936 (1.00)	0.00101 (0.171)	0.0609 (1.00)	0.0919 (1.00)	0.748 (1.00)	0.608 (1.00)

'amp_1p22.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S1. Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 1(1P22.3) MUTATED	4	3	14	51	24	15	2	2
AMP PEAK 1(1P22.3) WILD-TYPE	17	33	105	45	85	57	18	38

Figure S1. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S2. Gene #1: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 1(1P22.3) MUTATED	14	19	24	47	11
AMP PEAK 1(1P22.3) WILD-TYPE	87	133	90	41	47

Figure S2. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S3. Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 1(1P22.3) MUTATED	40	54	31	111	14
AMP PEAK 1(1P22.3) WILD-TYPE	220	358	62	154	35

Figure S3. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S4. Gene #1: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 1(1P22.3) MUTATED	72	30	33	11	23
AMP PEAK 1(1P22.3) WILD-TYPE	60	167	144	77	105

Figure S4. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.055

Table S5. Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 1(1P22.3) MUTATED	52	27	17
AMP PEAK 1(1P22.3) WILD-TYPE	97	105	100

Figure S5. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S6. Gene #1: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 1(1P22.3) MUTATED	15	14	45	17	5
AMP PEAK 1(1P22.3) WILD-TYPE	49	92	45	90	26

Figure S6. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S7. Gene #1: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 1(1P22.3) MUTATED	96	130	22
AMP PEAK 1(1P22.3) WILD-TYPE	447	168	210

Figure S7. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S8. Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 1(1P22.3) MUTATED	34	36	34	29	99	16
AMP PEAK 1(1P22.3) WILD-TYPE	185	128	272	112	84	44

Figure S8. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S9. Gene #1: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 1(1P22.3) MUTATED	126	42	79
AMP PEAK 1(1P22.3) WILD-TYPE	205	211	397

Figure S9. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S10. Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 1(1P22.3) MUTATED	37	42	50	29	9	80
AMP PEAK 1(1P22.3) WILD-TYPE	194	118	272	98	77	54

Figure S10. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S11. Gene #1: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 1(1P22.3) MUTATED	29	73	13	12	30
AMP PEAK 1(1P22.3) WILD-TYPE	151	66	86	99	103

Figure S11. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S12. Gene #1: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 1(1P22.3) MUTATED	97	48	12
AMP PEAK 1(1P22.3) WILD-TYPE	208	199	98

Figure S12. Get High-res Image Gene #1: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S13. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 2(1Q21.3) MUTATED	16	19	75	88	88	54	10	29
AMP PEAK 2(1Q21.3) WILD-TYPE	5	17	44	8	21	18	10	11

Figure S13. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 2(1Q21.3) MUTATED	62	102	89	81	45
AMP PEAK 2(1Q21.3) WILD-TYPE	39	50	25	7	13

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

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 2(1Q21.3) MUTATED	193	250	92	210	36
AMP PEAK 2(1Q21.3) WILD-TYPE	67	162	1	55	13

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S16. Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 2(1Q21.3) MUTATED	112	144	130	65	70
AMP PEAK 2(1Q21.3) WILD-TYPE	20	53	47	23	58

Figure S16. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.15

Table S17. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 2(1Q21.3) MUTATED	390	236	150
AMP PEAK 2(1Q21.3) WILD-TYPE	153	62	82

Figure S17. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S18. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 2(1Q21.3) MUTATED	137	131	202	112	159	35
AMP PEAK 2(1Q21.3) WILD-TYPE	82	33	104	29	24	25

Figure S18. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.095

Table S19. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 2(1Q21.3) MUTATED	263	166	335
AMP PEAK 2(1Q21.3) WILD-TYPE	68	87	141

Figure S19. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S20. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 2(1Q21.3) MUTATED	158	113	215	109	48	121
AMP PEAK 2(1Q21.3) WILD-TYPE	73	47	107	18	38	13

Figure S20. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.19

Table S21. Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 2(1Q21.3) MUTATED	125	114	70	64	90
AMP PEAK 2(1Q21.3) WILD-TYPE	55	25	29	47	43

Figure S21. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q44' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S22. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 3(1Q44) MUTATED	16	20	69	78	91	57	11	32
AMP PEAK 3(1Q44) WILD-TYPE	5	16	50	18	18	15	9	8

Figure S22. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.18

Table S23. Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 3(1Q44) MUTATED	59	107	92	72	44
AMP PEAK 3(1Q44) WILD-TYPE	42	45	22	16	14

Figure S23. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S24. Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 3(1Q44) MUTATED	197	263	93	203	33
AMP PEAK 3(1Q44) WILD-TYPE	63	149	0	62	16

Figure S24. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.032

Table S25. Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 3(1Q44) MUTATED	137	134	224	109	143	37
AMP PEAK 3(1Q44) WILD-TYPE	82	30	82	32	40	23

Figure S25. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.034

Table S26. Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 3(1Q44) MUTATED	157	118	235	109	50	104
AMP PEAK 3(1Q44) WILD-TYPE	74	42	87	18	36	30

Figure S26. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.13

Table S27. Gene #4: 'amp_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 4(3P25.1) MUTATED	6	7	34	20	18	25	7	1
AMP PEAK 4(3P25.1) WILD-TYPE	15	29	85	76	91	47	13	39

Figure S27. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3p25.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S28. Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 4(3P25.1) MUTATED	27	18	42	18	13
AMP PEAK 4(3P25.1) WILD-TYPE	74	134	72	70	45

Figure S28. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S29. Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 4(3P25.1) MUTATED	75	19	23	69	12
AMP PEAK 4(3P25.1) WILD-TYPE	185	393	70	196	37

Figure S29. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S30. Gene #4: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 4(3P25.1) MUTATED	34	19	38	10	14
AMP PEAK 4(3P25.1) WILD-TYPE	98	178	139	78	114

Figure S30. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S31. Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 4(3P25.1) MUTATED	110	77	10
AMP PEAK 4(3P25.1) WILD-TYPE	433	221	222

Figure S31. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S32. Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 4(3P25.1) MUTATED	45	53	29	14	43	13
AMP PEAK 4(3P25.1) WILD-TYPE	174	111	277	127	140	47

Figure S32. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S33. Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 4(3P25.1) MUTATED	86	29	75
AMP PEAK 4(3P25.1) WILD-TYPE	245	224	401

Figure S33. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S34. Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 4(3P25.1) MUTATED	58	38	28	22	11	33
AMP PEAK 4(3P25.1) WILD-TYPE	173	122	294	105	75	101

Figure S34. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S35. Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 5(3Q26.32) MUTATED	5	11	41	58	19	34	9	4
AMP PEAK 5(3Q26.32) WILD-TYPE	16	25	78	38	90	38	11	36

Figure S35. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S36. Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 5(3Q26.32) MUTATED	29	29	57	53	13
AMP PEAK 5(3Q26.32) WILD-TYPE	72	123	57	35	45

Figure S36. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S37. Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 5(3Q26.32) MUTATED	99	37	29	161	14
AMP PEAK 5(3Q26.32) WILD-TYPE	161	375	64	104	35

Figure S37. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S38. Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 5(3Q26.32) MUTATED	83	36	51	18	22
AMP PEAK 5(3Q26.32) WILD-TYPE	49	161	126	70	106

Figure S38. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S39. Gene #5: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 5(3Q26.32) MUTATED	76	36	30
AMP PEAK 5(3Q26.32) WILD-TYPE	73	96	87

Figure S39. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S40. Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 5(3Q26.32) MUTATED	22	26	54	30	10
AMP PEAK 5(3Q26.32) WILD-TYPE	42	80	36	77	21

Figure S40. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S41. Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 5(3Q26.32) MUTATED	151	165	21
AMP PEAK 5(3Q26.32) WILD-TYPE	392	133	211

Figure S41. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S42. Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 5(3Q26.32) MUTATED	62	68	50	16	116	25
AMP PEAK 5(3Q26.32) WILD-TYPE	157	96	256	125	67	35

Figure S42. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S43. Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 5(3Q26.32) MUTATED	174	46	111
AMP PEAK 5(3Q26.32) WILD-TYPE	157	207	365

Figure S43. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S44. Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 5(3Q26.32) MUTATED	72	71	52	32	19	85
AMP PEAK 5(3Q26.32) WILD-TYPE	159	89	270	95	67	49

Figure S44. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S45. Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 5(3Q26.32) MUTATED	52	77	14	21	29
AMP PEAK 5(3Q26.32) WILD-TYPE	128	62	85	90	104

Figure S45. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S46. Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 5(3Q26.32) MUTATED	119	49	25
AMP PEAK 5(3Q26.32) WILD-TYPE	186	198	85

Figure S46. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S47. Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 6(4Q13.3) MUTATED	4	3	32	18	3	18	4	3
AMP PEAK 6(4Q13.3) WILD-TYPE	17	33	87	78	106	54	16	37

Figure S47. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S48. Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 6(4Q13.3) MUTATED	22	12	31	18	2
AMP PEAK 6(4Q13.3) WILD-TYPE	79	140	83	70	56

Figure S48. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S49. Gene #6: 'amp_4q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 6(4Q13.3) MUTATED	73	22	2	59	7
AMP PEAK 6(4Q13.3) WILD-TYPE	187	390	91	206	42

Figure S49. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q13.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S50. Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 6(4Q13.3) MUTATED	32	16	37	5	11
AMP PEAK 6(4Q13.3) WILD-TYPE	100	181	140	83	117

Figure S50. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S51. Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 6(4Q13.3) MUTATED	83	68	12
AMP PEAK 6(4Q13.3) WILD-TYPE	460	230	220

Figure S51. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S52. Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 6(4Q13.3) MUTATED	45	34	24	3	39	18
AMP PEAK 6(4Q13.3) WILD-TYPE	174	130	282	138	144	42

Figure S52. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S53. Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 6(4Q13.3) MUTATED	78	20	63
AMP PEAK 6(4Q13.3) WILD-TYPE	253	233	413

Figure S53. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S54. Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 6(4Q13.3) MUTATED	46	42	21	10	12	30
AMP PEAK 6(4Q13.3) WILD-TYPE	185	118	301	117	74	104

Figure S54. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S55. Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 6(4Q13.3) MUTATED	65	22	10
AMP PEAK 6(4Q13.3) WILD-TYPE	240	225	100

Figure S55. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00085 (Fisher's exact test), Q value = 0.15

Table S56. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 7(5P15.33) MUTATED	34	44	59	40	17
AMP PEAK 7(5P15.33) WILD-TYPE	67	108	55	48	41

Figure S56. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S57. Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 7(5P15.33) MUTATED	123	65	50	137	18
AMP PEAK 7(5P15.33) WILD-TYPE	137	347	43	128	31

Figure S57. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S58. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 7(5P15.33) MUTATED	69	55	76	25	30
AMP PEAK 7(5P15.33) WILD-TYPE	63	142	101	63	98

Figure S58. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S59. Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 7(5P15.33) MUTATED	190	140	60
AMP PEAK 7(5P15.33) WILD-TYPE	353	158	172

Figure S59. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S60. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 7(5P15.33) MUTATED	79	79	81	36	89	26
AMP PEAK 7(5P15.33) WILD-TYPE	140	85	225	105	94	34

Figure S60. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S61. Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 7(5P15.33) MUTATED	155	69	159
AMP PEAK 7(5P15.33) WILD-TYPE	176	184	317

Figure S61. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S62. Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 7(5P15.33) MUTATED	85	70	81	52	31	64
AMP PEAK 7(5P15.33) WILD-TYPE	146	90	241	75	55	70

Figure S62. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S63. Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 8(6P23) MUTATED	3	7	30	49	18	28	9	6
AMP PEAK 8(6P23) WILD-TYPE	18	29	89	47	91	44	11	34

Figure S63. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S64. Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 8(6P23) MUTATED	22	28	48	45	7
AMP PEAK 8(6P23) WILD-TYPE	79	124	66	43	51

Figure S64. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S65. Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 8(6P23) MUTATED	84	29	22	147	16
AMP PEAK 8(6P23) WILD-TYPE	176	383	71	118	33

Figure S65. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S66. Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 8(6P23) MUTATED	74	29	59	7	23
AMP PEAK 8(6P23) WILD-TYPE	58	168	118	81	105

Figure S66. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S67. Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 8(6P23) MUTATED	68	24	24
AMP PEAK 8(6P23) WILD-TYPE	81	108	93

Figure S67. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S68. Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 8(6P23) MUTATED	14	21	46	27	8
AMP PEAK 8(6P23) WILD-TYPE	50	85	44	80	23

Figure S68. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S69. Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 8(6P23) MUTATED	132	142	23
AMP PEAK 8(6P23) WILD-TYPE	411	156	209

Figure S69. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S70. Gene #8: 'amp_6p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 8(6P23) MUTATED	46	71	50	15	97	18
AMP PEAK 8(6P23) WILD-TYPE	173	93	256	126	86	42

Figure S70. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S71. Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 8(6P23) MUTATED	159	34	93
AMP PEAK 8(6P23) WILD-TYPE	172	219	383

Figure S71. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S72. Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 8(6P23) MUTATED	73	63	35	26	17	72
AMP PEAK 8(6P23) WILD-TYPE	158	97	287	101	69	62

Figure S72. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S73. Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 8(6P23) MUTATED	42	67	21	12	24
AMP PEAK 8(6P23) WILD-TYPE	138	72	78	99	109

Figure S73. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S74. Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 8(6P23) MUTATED	110	44	12
AMP PEAK 8(6P23) WILD-TYPE	195	203	98

Figure S74. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S75. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 9(6Q21) MUTATED	4	1	11	42	11	24	9	2
AMP PEAK 9(6Q21) WILD-TYPE	17	35	108	54	98	48	11	38

Figure S75. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6q21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S76. Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 9(6Q21) MUTATED	10	14	39	37	4
AMP PEAK 9(6Q21) WILD-TYPE	91	138	75	51	54

Figure S76. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S77. Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 9(6Q21) MUTATED	23	25	17	130	6
AMP PEAK 9(6Q21) WILD-TYPE	237	387	76	135	43

Figure S77. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S78. Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 9(6Q21) MUTATED	61	9	31	6	20
AMP PEAK 9(6Q21) WILD-TYPE	71	188	146	82	108

Figure S78. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S79. Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 9(6Q21) MUTATED	55	11	16
AMP PEAK 9(6Q21) WILD-TYPE	94	121	101

Figure S79. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S80. Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 9(6Q21) MUTATED	6	15	38	16	7
AMP PEAK 9(6Q21) WILD-TYPE	58	91	52	91	24

Figure S80. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S81. Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 9(6Q21) MUTATED	67	123	10
AMP PEAK 9(6Q21) WILD-TYPE	476	175	222

Figure S81. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S82. Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 9(6Q21) MUTATED	22	47	22	7	82	20
AMP PEAK 9(6Q21) WILD-TYPE	197	117	284	134	101	40

Figure S82. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S83. Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 9(6Q21) MUTATED	129	20	42
AMP PEAK 9(6Q21) WILD-TYPE	202	233	434

Figure S83. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S84. Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 9(6Q21) MUTATED	44	58	14	14	3	58
AMP PEAK 9(6Q21) WILD-TYPE	187	102	308	113	83	76

Figure S84. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S85. Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 9(6Q21) MUTATED	21	68	8	7	16
AMP PEAK 9(6Q21) WILD-TYPE	159	71	91	104	117

Figure S85. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S86. Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 9(6Q21) MUTATED	85	26	9
AMP PEAK 9(6Q21) WILD-TYPE	220	221	101

Figure S86. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S87. Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 10(8P11.23) MUTATED	11	18	74	33	36	23	5	9
AMP PEAK 10(8P11.23) WILD-TYPE	10	18	45	63	73	49	15	31

Figure S87. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S88. Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 10(8P11.23) MUTATED	64	62	41	30	12
AMP PEAK 10(8P11.23) WILD-TYPE	37	90	73	58	46

Figure S88. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S89. Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 10(8P11.23) MUTATED	133	112	37	81	48
AMP PEAK 10(8P11.23) WILD-TYPE	127	300	56	184	1

Figure S89. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.036

Table S90. Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 10(8P11.23) MUTATED	47	66	92	32	35
AMP PEAK 10(8P11.23) WILD-TYPE	85	131	85	56	93

Figure S90. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S91. Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 10(8P11.23) MUTATED	28	47	32	54	2
AMP PEAK 10(8P11.23) WILD-TYPE	36	59	58	53	29

Figure S91. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S92. Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 10(8P11.23) MUTATED	246	95	66
AMP PEAK 10(8P11.23) WILD-TYPE	297	203	166

Figure S92. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S93. Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 10(8P11.23) MUTATED	132	73	98	31	59	14
AMP PEAK 10(8P11.23) WILD-TYPE	87	91	208	110	124	46

Figure S93. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S94. Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 11(8P11.21) MUTATED	119	105	41	106	49
AMP PEAK 11(8P11.21) WILD-TYPE	141	307	52	159	0

Figure S94. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S95. Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 11(8P11.21) MUTATED	71	65	81	28	38
AMP PEAK 11(8P11.21) WILD-TYPE	61	132	96	60	90

Figure S95. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S96. Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 11(8P11.21) MUTATED	226	133	57
AMP PEAK 11(8P11.21) WILD-TYPE	317	165	175

Figure S96. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S97. Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 11(8P11.21) MUTATED	119	71	86	31	93	16
AMP PEAK 11(8P11.21) WILD-TYPE	100	93	220	110	90	44

Figure S97. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.24

Table S98. Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 11(8P11.21) MUTATED	153	81	177
AMP PEAK 11(8P11.21) WILD-TYPE	178	172	299

Figure S98. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S99. Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 11(8P11.21) MUTATED	96	53	96	52	41	73
AMP PEAK 11(8P11.21) WILD-TYPE	135	107	226	75	45	61

Figure S99. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S100. Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 11(8P11.21) MUTATED	68	74	31	29	41
AMP PEAK 11(8P11.21) WILD-TYPE	112	65	68	82	92

Figure S100. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00088 (Fisher's exact test), Q value = 0.15

Table S101. Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 11(8P11.21) MUTATED	134	80	29
AMP PEAK 11(8P11.21) WILD-TYPE	171	167	81

Figure S101. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S102. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 12(8Q24.21) MUTATED	17	20	96	83	46	56	17	15
AMP PEAK 12(8Q24.21) WILD-TYPE	4	16	23	13	63	16	3	25

Figure S102. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S103. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 12(8Q24.21) MUTATED	84	83	92	75	16
AMP PEAK 12(8Q24.21) WILD-TYPE	17	69	22	13	42

Figure S103. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S104. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 12(8Q24.21) MUTATED	200	147	43	240	47
AMP PEAK 12(8Q24.21) WILD-TYPE	60	265	50	25	2

Figure S104. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S105. Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 12(8Q24.21) MUTATED	120	82	125	39	68
AMP PEAK 12(8Q24.21) WILD-TYPE	12	115	52	49	60

Figure S105. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S106. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 12(8Q24.21) MUTATED	126	71	76
AMP PEAK 12(8Q24.21) WILD-TYPE	23	61	41

Figure S106. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S107. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 12(8Q24.21) MUTATED	34	57	78	79	25
AMP PEAK 12(8Q24.21) WILD-TYPE	30	49	12	28	6

Figure S107. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S108. Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 12(8Q24.21) MUTATED	338	250	85
AMP PEAK 12(8Q24.21) WILD-TYPE	205	48	147

Figure S108. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S109. Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 12(8Q24.21) MUTATED	168	126	140	33	162	44
AMP PEAK 12(8Q24.21) WILD-TYPE	51	38	166	108	21	16

Figure S109. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S110. Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 12(8Q24.21) MUTATED	291	111	260
AMP PEAK 12(8Q24.21) WILD-TYPE	40	142	216

Figure S110. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S111. Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 12(8Q24.21) MUTATED	162	124	125	77	52	122
AMP PEAK 12(8Q24.21) WILD-TYPE	69	36	197	50	34	12

Figure S111. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S112. Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 12(8Q24.21) MUTATED	114	128	41	44	65
AMP PEAK 12(8Q24.21) WILD-TYPE	66	11	58	67	68

Figure S112. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S113. Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 12(8Q24.21) MUTATED	224	116	52
AMP PEAK 12(8Q24.21) WILD-TYPE	81	131	58

Figure S113. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S114. Gene #13: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 13(10P15.1) MUTATED	6	4	26	67	12	33	6	7
AMP PEAK 13(10P15.1) WILD-TYPE	15	32	93	29	97	39	14	33

Figure S114. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S115. Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 13(10P15.1) MUTATED	16	22	53	63	7
AMP PEAK 13(10P15.1) WILD-TYPE	85	130	61	25	51

Figure S115. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S116. Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 13(10P15.1) MUTATED	72	38	16	168	10
AMP PEAK 13(10P15.1) WILD-TYPE	188	374	77	97	39

Figure S116. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S117. Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 13(10P15.1) MUTATED	88	16	45	9	31
AMP PEAK 13(10P15.1) WILD-TYPE	44	181	132	79	97

Figure S117. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S118. Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 13(10P15.1) MUTATED	78	22	29
AMP PEAK 13(10P15.1) WILD-TYPE	71	110	88

Figure S118. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S119. Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 13(10P15.1) MUTATED	8	24	61	27	9
AMP PEAK 13(10P15.1) WILD-TYPE	56	82	29	80	22

Figure S119. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S120. Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 13(10P15.1) MUTATED	106	172	26
AMP PEAK 13(10P15.1) WILD-TYPE	437	126	206

Figure S120. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S121. Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 13(10P15.1) MUTATED	48	56	43	6	125	26
AMP PEAK 13(10P15.1) WILD-TYPE	171	108	263	135	58	34

Figure S121. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S122. Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 13(10P15.1) MUTATED	180	33	83
AMP PEAK 13(10P15.1) WILD-TYPE	151	220	393

Figure S122. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S123. Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 13(10P15.1) MUTATED	67	75	31	25	8	90
AMP PEAK 13(10P15.1) WILD-TYPE	164	85	291	102	78	44

Figure S123. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S124. Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 13(10P15.1) MUTATED	35	89	16	11	25
AMP PEAK 13(10P15.1) WILD-TYPE	145	50	83	100	108

Figure S124. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S125. Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 13(10P15.1) MUTATED	126	36	14
AMP PEAK 13(10P15.1) WILD-TYPE	179	211	96

Figure S125. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S126. Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 14(10Q22.3) MUTATED	6	3	16	18	9	23	8	3
AMP PEAK 14(10Q22.3) WILD-TYPE	15	33	103	78	100	49	12	37

Figure S126. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S127. Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 14(10Q22.3) MUTATED	11	17	36	17	5
AMP PEAK 14(10Q22.3) WILD-TYPE	90	135	78	71	53

Figure S127. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S128. Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 14(10Q22.3) MUTATED	42	24	11	67	6
AMP PEAK 14(10Q22.3) WILD-TYPE	218	388	82	198	43

Figure S128. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S129. Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 14(10Q22.3) MUTATED	69	67	14
AMP PEAK 14(10Q22.3) WILD-TYPE	474	231	218

Figure S129. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S130. Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 14(10Q22.3) MUTATED	30	36	31	4	32	17
AMP PEAK 14(10Q22.3) WILD-TYPE	189	128	275	137	151	43

Figure S130. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S131. Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 14(10Q22.3) MUTATED	69	18	59
AMP PEAK 14(10Q22.3) WILD-TYPE	262	235	417

Figure S131. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S132. Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 14(10Q22.3) MUTATED	45	33	18	20	6	24
AMP PEAK 14(10Q22.3) WILD-TYPE	186	127	304	107	80	110

Figure S132. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.16

Table S133. Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 15(11P13) MUTATED	28	26	34	25	4
AMP PEAK 15(11P13) WILD-TYPE	73	126	80	63	54

Figure S133. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S134. Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 15(11P13) MUTATED	80	30	16	88	8
AMP PEAK 15(11P13) WILD-TYPE	180	382	77	177	41

Figure S134. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S135. Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 15(11P13) MUTATED	114	87	21
AMP PEAK 15(11P13) WILD-TYPE	429	211	211

Figure S135. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S136. Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 15(11P13) MUTATED	53	44	47	9	59	10
AMP PEAK 15(11P13) WILD-TYPE	166	120	259	132	124	50

Figure S136. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S137. Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 15(11P13) MUTATED	102	23	94
AMP PEAK 15(11P13) WILD-TYPE	229	230	382

Figure S137. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S138. Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 15(11P13) MUTATED	61	53	35	19	13	38
AMP PEAK 15(11P13) WILD-TYPE	170	107	287	108	73	96

Figure S138. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.029

Table S139. Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 15(11P13) MUTATED	41	42	12	16	14
AMP PEAK 15(11P13) WILD-TYPE	139	97	87	95	119

Figure S139. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.032

Table S140. Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 15(11P13) MUTATED	79	29	17
AMP PEAK 15(11P13) WILD-TYPE	226	218	93

Figure S140. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.034

Table S141. Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 16(11Q13.3) MUTATED	13	18	62	28	33	37	11	13
AMP PEAK 16(11Q13.3) WILD-TYPE	8	18	57	68	76	35	9	27

Figure S141. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S142. Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 16(11Q13.3) MUTATED	55	57	68	24	11
AMP PEAK 16(11Q13.3) WILD-TYPE	46	95	46	64	47

Figure S142. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S143. Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 16(11Q13.3) MUTATED	183	67	28	101	18
AMP PEAK 16(11Q13.3) WILD-TYPE	77	345	65	164	31

Figure S143. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S144. Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 16(11Q13.3) MUTATED	48	60	95	22	25
AMP PEAK 16(11Q13.3) WILD-TYPE	84	137	82	66	103

Figure S144. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.11

Table S145. Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 16(11Q13.3) MUTATED	17	49	29	60	13
AMP PEAK 16(11Q13.3) WILD-TYPE	47	57	61	47	18

Figure S145. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S146. Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 16(11Q13.3) MUTATED	228	109	60
AMP PEAK 16(11Q13.3) WILD-TYPE	315	189	172

Figure S146. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S147. Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 16(11Q13.3) MUTATED	112	83	100	24	58	20
AMP PEAK 16(11Q13.3) WILD-TYPE	107	81	206	117	125	40

Figure S147. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.027

Table S148. Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 17(11Q14.1) MUTATED	30	36	45	30	5
AMP PEAK 17(11Q14.1) WILD-TYPE	71	116	69	58	53

Figure S148. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S149. Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 17(11Q14.1) MUTATED	102	38	19	97	10
AMP PEAK 17(11Q14.1) WILD-TYPE	158	374	74	168	39

Figure S149. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S150. Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 17(11Q14.1) MUTATED	43	32	52	18	16
AMP PEAK 17(11Q14.1) WILD-TYPE	89	165	125	70	112

Figure S150. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S151. Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 17(11Q14.1) MUTATED	133	99	34
AMP PEAK 17(11Q14.1) WILD-TYPE	410	199	198

Figure S151. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S152. Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 17(11Q14.1) MUTATED	55	56	60	17	61	17
AMP PEAK 17(11Q14.1) WILD-TYPE	164	108	246	124	122	43

Figure S152. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S153. Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 17(11Q14.1) MUTATED	116	38	106
AMP PEAK 17(11Q14.1) WILD-TYPE	215	215	370

Figure S153. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.056

Table S154. Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 17(11Q14.1) MUTATED	62	50	56	28	17	47
AMP PEAK 17(11Q14.1) WILD-TYPE	169	110	266	99	69	87

Figure S154. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S155. Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 18(12P13.33) MUTATED	3	4	36	53	18	29	3	3
AMP PEAK 18(12P13.33) WILD-TYPE	18	32	83	43	91	43	17	37

Figure S155. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S156. Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 18(12P13.33) MUTATED	30	16	44	49	10
AMP PEAK 18(12P13.33) WILD-TYPE	71	136	70	39	48

Figure S156. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S157. Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 18(12P13.33) MUTATED	84	22	27	135	13
AMP PEAK 18(12P13.33) WILD-TYPE	176	390	66	130	36

Figure S157. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S158. Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 18(12P13.33) MUTATED	71	36	44	10	16
AMP PEAK 18(12P13.33) WILD-TYPE	61	161	133	78	112

Figure S158. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S159. Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 18(12P13.33) MUTATED	71	30	19
AMP PEAK 18(12P13.33) WILD-TYPE	78	102	98

Figure S159. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S160. Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 18(12P13.33) MUTATED	15	15	47	33	10
AMP PEAK 18(12P13.33) WILD-TYPE	49	91	43	74	21

Figure S160. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S161. Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 18(12P13.33) MUTATED	126	135	20
AMP PEAK 18(12P13.33) WILD-TYPE	417	163	212

Figure S161. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S162. Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 18(12P13.33) MUTATED	57	58	38	12	102	14
AMP PEAK 18(12P13.33) WILD-TYPE	162	106	268	129	81	46

Figure S162. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S163. Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 18(12P13.33) MUTATED	153	34	85
AMP PEAK 18(12P13.33) WILD-TYPE	178	219	391

Figure S163. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S164. Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 18(12P13.33) MUTATED	63	49	41	29	13	77
AMP PEAK 18(12P13.33) WILD-TYPE	168	111	281	98	73	57

Figure S164. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S165. Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 18(12P13.33) MUTATED	39	68	15	12	24
AMP PEAK 18(12P13.33) WILD-TYPE	141	71	84	99	109

Figure S165. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S166. Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 18(12P13.33) MUTATED	99	44	15
AMP PEAK 18(12P13.33) WILD-TYPE	206	203	95

Figure S166. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S167. Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 19(12Q15) MUTATED	4	6	54	21	20	35	7	6
AMP PEAK 19(12Q15) WILD-TYPE	17	30	65	75	89	37	13	34

Figure S167. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S168. Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 19(12Q15) MUTATED	43	24	56	18	12
AMP PEAK 19(12Q15) WILD-TYPE	58	128	58	70	46

Figure S168. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S169. Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 19(12Q15) MUTATED	133	31	29	70	12
AMP PEAK 19(12Q15) WILD-TYPE	127	381	64	195	37

Figure S169. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S170. Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 19(12Q15) MUTATED	24	50	61	13	20
AMP PEAK 19(12Q15) WILD-TYPE	108	147	116	75	108

Figure S170. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S171. Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 19(12Q15) MUTATED	183	62	29
AMP PEAK 19(12Q15) WILD-TYPE	360	236	203

Figure S171. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S172. Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 19(12Q15) MUTATED	81	79	52	20	30	12
AMP PEAK 19(12Q15) WILD-TYPE	138	85	254	121	153	48

Figure S172. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S173. Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 19(12Q15) MUTATED	98	39	132
AMP PEAK 19(12Q15) WILD-TYPE	233	214	344

Figure S173. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S174. Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 19(12Q15) MUTATED	93	43	57	32	22	22
AMP PEAK 19(12Q15) WILD-TYPE	138	117	265	95	64	112

Figure S174. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S175. Gene #19: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 19(12Q15) MUTATED	65	24	23	14	28
AMP PEAK 19(12Q15) WILD-TYPE	115	115	76	97	105

Figure S175. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S176. Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 20(13Q34) MUTATED	3	5	19	43	16	10	4	0
AMP PEAK 20(13Q34) WILD-TYPE	18	31	100	53	93	62	16	40

Figure S176. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S177. Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 20(13Q34) MUTATED	17	14	23	38	8
AMP PEAK 20(13Q34) WILD-TYPE	84	138	91	50	50

Figure S177. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S178. Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 20(13Q34) MUTATED	38	23	14	97	7
AMP PEAK 20(13Q34) WILD-TYPE	222	389	79	168	42

Figure S178. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S179. Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 20(13Q34) MUTATED	50	17	24	5	14
AMP PEAK 20(13Q34) WILD-TYPE	82	180	153	83	114

Figure S179. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S180. Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 20(13Q34) MUTATED	50	22	12
AMP PEAK 20(13Q34) WILD-TYPE	99	110	105

Figure S180. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S181. Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 20(13Q34) MUTATED	10	9	39	17	9
AMP PEAK 20(13Q34) WILD-TYPE	54	97	51	90	22

Figure S181. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S182. Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 20(13Q34) MUTATED	67	101	11
AMP PEAK 20(13Q34) WILD-TYPE	476	197	221

Figure S182. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S183. Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 20(13Q34) MUTATED	31	22	21	13	74	18
AMP PEAK 20(13Q34) WILD-TYPE	188	142	285	128	109	42

Figure S183. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S184. Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 20(13Q34) MUTATED	109	22	45
AMP PEAK 20(13Q34) WILD-TYPE	222	231	431

Figure S184. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S185. Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 20(13Q34) MUTATED	31	46	20	15	8	56
AMP PEAK 20(13Q34) WILD-TYPE	200	114	302	112	78	78

Figure S185. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S186. Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 20(13Q34) MUTATED	19	47	6	8	17
AMP PEAK 20(13Q34) WILD-TYPE	161	92	93	103	116

Figure S186. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S187. Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 20(13Q34) MUTATED	66	23	8
AMP PEAK 20(13Q34) WILD-TYPE	239	224	102

Figure S187. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S188. Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 21(14Q21.1) MUTATED	5	9	33	11	21	26	6	0
AMP PEAK 21(14Q21.1) WILD-TYPE	16	27	86	85	88	46	14	40

Figure S188. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S189. Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 21(14Q21.1) MUTATED	29	24	42	8	8
AMP PEAK 21(14Q21.1) WILD-TYPE	72	128	72	80	50

Figure S189. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S190. Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 21(14Q21.1) MUTATED	97	36	22	54	11
AMP PEAK 21(14Q21.1) WILD-TYPE	163	376	71	211	38

Figure S190. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q21.1' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S191. Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 21(14Q21.1) MUTATED	17	33	55	12	15
AMP PEAK 21(14Q21.1) WILD-TYPE	115	164	122	76	113

Figure S191. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S192. Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 21(14Q21.1) MUTATED	150	47	21
AMP PEAK 21(14Q21.1) WILD-TYPE	393	251	211

Figure S192. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S193. Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 21(14Q21.1) MUTATED	59	72	36	18	17	16
AMP PEAK 21(14Q21.1) WILD-TYPE	160	92	270	123	166	44

Figure S193. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S194. Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 21(14Q21.1) MUTATED	69	53	40	32	9	11
AMP PEAK 21(14Q21.1) WILD-TYPE	162	107	282	95	77	123

Figure S194. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S195. Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 22(15Q26.3) MUTATED	3	8	31	32	4	16	8	2
AMP PEAK 22(15Q26.3) WILD-TYPE	18	28	88	64	105	56	12	38

Figure S195. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S196. Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 22(15Q26.3) MUTATED	23	23	25	30	3
AMP PEAK 22(15Q26.3) WILD-TYPE	78	129	89	58	55

Figure S196. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S197. Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 22(15Q26.3) MUTATED	63	30	6	91	4
AMP PEAK 22(15Q26.3) WILD-TYPE	197	382	87	174	45

Figure S197. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00117 (Fisher's exact test), Q value = 0.19

Table S198. Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 22(15Q26.3) MUTATED	36	19	27	14	17
AMP PEAK 22(15Q26.3) WILD-TYPE	96	178	150	74	111

Figure S198. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S199. Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 22(15Q26.3) MUTATED	92	85	16
AMP PEAK 22(15Q26.3) WILD-TYPE	451	213	216

Figure S199. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S200. Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 22(15Q26.3) MUTATED	50	33	29	13	62	6
AMP PEAK 22(15Q26.3) WILD-TYPE	169	131	277	128	121	54

Figure S200. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S201. Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 22(15Q26.3) MUTATED	92	28	67
AMP PEAK 22(15Q26.3) WILD-TYPE	239	225	409

Figure S201. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S202. Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 22(15Q26.3) MUTATED	42	44	27	16	15	43
AMP PEAK 22(15Q26.3) WILD-TYPE	189	116	295	111	71	91

Figure S202. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S203. Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 22(15Q26.3) MUTATED	75	28	12
AMP PEAK 22(15Q26.3) WILD-TYPE	230	219	98

Figure S203. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S204. Gene #23: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 23(17P11.2) MUTATED	62	23	13	35	13
AMP PEAK 23(17P11.2) WILD-TYPE	198	389	80	230	36

Figure S204. Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17p11.2' versus 'METHLYATION_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.13

Table S205. Gene #23: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 23(17P11.2) MUTATED	22	30	39	7	8
AMP PEAK 23(17P11.2) WILD-TYPE	110	167	138	81	120

Figure S205. Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.086

Table S206. Gene #23: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 23(17P11.2) MUTATED	91	38	15
AMP PEAK 23(17P11.2) WILD-TYPE	452	260	217

Figure S206. Get High-res Image Gene #23: 'amp_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S207. Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 24(17Q12) MUTATED	9	11	53	19	14	49	7	4
AMP PEAK 24(17Q12) WILD-TYPE	12	25	66	77	95	23	13	36

Figure S207. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S208. Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 24(17Q12) MUTATED	40	28	71	16	11
AMP PEAK 24(17Q12) WILD-TYPE	61	124	43	72	47

Figure S208. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S209. Gene #24: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 24(17Q12) MUTATED	171	59	21	66	15
AMP PEAK 24(17Q12) WILD-TYPE	89	353	72	199	34

Figure S209. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S210. Gene #24: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 24(17Q12) MUTATED	33	46	85	23	29
AMP PEAK 24(17Q12) WILD-TYPE	99	151	92	65	99

Figure S210. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S211. Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 24(17Q12) MUTATED	9	28	20	41	31
AMP PEAK 24(17Q12) WILD-TYPE	55	78	70	66	0

Figure S211. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S212. Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 24(17Q12) MUTATED	191	104	35
AMP PEAK 24(17Q12) WILD-TYPE	352	194	197

Figure S212. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S213. Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 24(17Q12) MUTATED	94	86	58	19	33	40
AMP PEAK 24(17Q12) WILD-TYPE	125	78	248	122	150	20

Figure S213. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S214. Gene #24: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 24(17Q12) MUTATED	101	71	73	32	26	22
AMP PEAK 24(17Q12) WILD-TYPE	130	89	249	95	60	112

Figure S214. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.059

Table S215. Gene #24: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 24(17Q12) MUTATED	77	38	19	29	37
AMP PEAK 24(17Q12) WILD-TYPE	103	101	80	82	96

Figure S215. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.038

Table S216. Gene #24: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 24(17Q12) MUTATED	117	58	25
AMP PEAK 24(17Q12) WILD-TYPE	188	189	85

Figure S216. Get High-res Image Gene #24: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S217. Gene #25: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 25(17Q23.1) MUTATED	9	17	81	29	16	44	11	9
AMP PEAK 25(17Q23.1) WILD-TYPE	12	19	38	67	93	28	9	31

Figure S217. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S218. Gene #25: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 25(17Q23.1) MUTATED	62	45	71	25	13
AMP PEAK 25(17Q23.1) WILD-TYPE	39	107	43	63	45

Figure S218. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S219. Gene #25: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 25(17Q23.1) MUTATED	201	68	23	113	20
AMP PEAK 25(17Q23.1) WILD-TYPE	59	344	70	152	29

Figure S219. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S220. Gene #25: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 25(17Q23.1) MUTATED	52	61	99	28	40
AMP PEAK 25(17Q23.1) WILD-TYPE	80	136	78	60	88

Figure S220. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S221. Gene #25: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 25(17Q23.1) MUTATED	13	40	26	68	19
AMP PEAK 25(17Q23.1) WILD-TYPE	51	66	64	39	12

Figure S221. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S222. Gene #25: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 25(17Q23.1) MUTATED	249	122	52
AMP PEAK 25(17Q23.1) WILD-TYPE	294	176	180

Figure S222. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S223. Gene #25: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 25(17Q23.1) MUTATED	126	100	88	20	60	29
AMP PEAK 25(17Q23.1) WILD-TYPE	93	64	218	121	123	31

Figure S223. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S224. Gene #25: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 25(17Q23.1) MUTATED	166	64	187
AMP PEAK 25(17Q23.1) WILD-TYPE	165	189	289

Figure S224. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S225. Gene #25: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 25(17Q23.1) MUTATED	126	84	93	34	36	44
AMP PEAK 25(17Q23.1) WILD-TYPE	105	76	229	93	50	90

Figure S225. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S226. Gene #25: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 25(17Q23.1) MUTATED	88	58	26	27	47
AMP PEAK 25(17Q23.1) WILD-TYPE	92	81	73	84	86

Figure S226. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S227. Gene #25: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 25(17Q23.1) MUTATED	150	67	29
AMP PEAK 25(17Q23.1) WILD-TYPE	155	180	81

Figure S227. Get High-res Image Gene #25: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S228. Gene #26: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 26(19P13.12) MUTATED	5	6	22	40	16	11	5	4
AMP PEAK 26(19P13.12) WILD-TYPE	16	30	97	56	93	61	15	36

Figure S228. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.045

Table S229. Gene #26: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 26(19P13.12) MUTATED	19	21	23	35	11
AMP PEAK 26(19P13.12) WILD-TYPE	82	131	91	53	47

Figure S229. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S230. Gene #26: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 26(19P13.12) MUTATED	49	38	29	100	13
AMP PEAK 26(19P13.12) WILD-TYPE	211	374	64	165	36

Figure S230. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S231. Gene #26: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 26(19P13.12) MUTATED	47	25	31	16	26
AMP PEAK 26(19P13.12) WILD-TYPE	85	172	146	72	102

Figure S231. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.16

Table S232. Gene #26: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 26(19P13.12) MUTATED	49	25	17
AMP PEAK 26(19P13.12) WILD-TYPE	100	107	100

Figure S232. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S233. Gene #26: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 26(19P13.12) MUTATED	88	102	37
AMP PEAK 26(19P13.12) WILD-TYPE	455	196	195

Figure S233. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S234. Gene #26: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 26(19P13.12) MUTATED	39	30	54	15	74	15
AMP PEAK 26(19P13.12) WILD-TYPE	180	134	252	126	109	45

Figure S234. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S235. Gene #26: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 26(19P13.12) MUTATED	105	48	70
AMP PEAK 26(19P13.12) WILD-TYPE	226	205	406

Figure S235. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S236. Gene #26: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 26(19P13.12) MUTATED	44	42	53	18	10	56
AMP PEAK 26(19P13.12) WILD-TYPE	187	118	269	109	76	78

Figure S236. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S237. Gene #26: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 26(19P13.12) MUTATED	27	54	16	27	18
AMP PEAK 26(19P13.12) WILD-TYPE	153	85	83	84	115

Figure S237. Get High-res Image Gene #26: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S238. Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 27(19Q12) MUTATED	4	5	29	55	15	20	7	5
AMP PEAK 27(19Q12) WILD-TYPE	17	31	90	41	94	52	13	35

Figure S238. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S239. Gene #27: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 27(19Q12) MUTATED	20	24	35	50	11
AMP PEAK 27(19Q12) WILD-TYPE	81	128	79	38	47

Figure S239. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S240. Gene #27: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 27(19Q12) MUTATED	55	39	30	143	16
AMP PEAK 27(19Q12) WILD-TYPE	205	373	63	122	33

Figure S240. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S241. Gene #27: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 27(19Q12) MUTATED	69	29	43	15	25
AMP PEAK 27(19Q12) WILD-TYPE	63	168	134	73	103

Figure S241. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S242. Gene #27: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 27(19Q12) MUTATED	64	22	24
AMP PEAK 27(19Q12) WILD-TYPE	85	110	93

Figure S242. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S243. Gene #27: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 27(19Q12) MUTATED	15	21	46	18	10
AMP PEAK 27(19Q12) WILD-TYPE	49	85	44	89	21

Figure S243. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S244. Gene #27: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 27(19Q12) MUTATED	107	140	35
AMP PEAK 27(19Q12) WILD-TYPE	436	158	197

Figure S244. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S245. Gene #27: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 27(19Q12) MUTATED	45	44	51	15	104	23
AMP PEAK 27(19Q12) WILD-TYPE	174	120	255	126	79	37

Figure S245. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S246. Gene #27: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 27(19Q12) MUTATED	153	46	80
AMP PEAK 27(19Q12) WILD-TYPE	178	207	396

Figure S246. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S247. Gene #27: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 27(19Q12) MUTATED	61	61	51	19	12	75
AMP PEAK 27(19Q12) WILD-TYPE	170	99	271	108	74	59

Figure S247. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S248. Gene #27: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 27(19Q12) MUTATED	37	72	16	25	26
AMP PEAK 27(19Q12) WILD-TYPE	143	67	83	86	107

Figure S248. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.18

Table S249. Gene #27: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 27(19Q12) MUTATED	102	52	22
AMP PEAK 27(19Q12) WILD-TYPE	203	195	88

Figure S249. Get High-res Image Gene #27: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.077

Table S250. Gene #28: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 28(19Q13.42) MUTATED	5	8	36	40	17	20	10	6
AMP PEAK 28(19Q13.42) WILD-TYPE	16	28	83	56	92	52	10	34

Figure S250. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S251. Gene #28: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 28(19Q13.42) MUTATED	74	42	30	109	20
AMP PEAK 28(19Q13.42) WILD-TYPE	186	370	63	156	29

Figure S251. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.42' versus 'METHLYATION_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.16

Table S252. Gene #28: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 28(19Q13.42) MUTATED	42	35	56	19	21
AMP PEAK 28(19Q13.42) WILD-TYPE	90	162	121	69	107

Figure S252. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.42' versus 'RPPA_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.19

Table S253. Gene #28: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 28(19Q13.42) MUTATED	57	26	27
AMP PEAK 28(19Q13.42) WILD-TYPE	92	106	90

Figure S253. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S254. Gene #28: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 28(19Q13.42) MUTATED	136	98	40
AMP PEAK 28(19Q13.42) WILD-TYPE	407	200	192

Figure S254. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S255. Gene #28: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 28(19Q13.42) MUTATED	62	51	63	16	63	19
AMP PEAK 28(19Q13.42) WILD-TYPE	157	113	243	125	120	41

Figure S255. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.42' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S256. Gene #28: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 28(19Q13.42) MUTATED	119	49	103
AMP PEAK 28(19Q13.42) WILD-TYPE	212	204	373

Figure S256. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S257. Gene #28: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 28(19Q13.42) MUTATED	71	59	61	20	16	44
AMP PEAK 28(19Q13.42) WILD-TYPE	160	101	261	107	70	90

Figure S257. Get High-res Image Gene #28: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S258. Gene #29: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 29(20Q13.2) MUTATED	12	18	85	52	35	49	15	10
AMP PEAK 29(20Q13.2) WILD-TYPE	9	18	34	44	74	23	5	30

Figure S258. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S259. Gene #29: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 29(20Q13.2) MUTATED	73	56	86	44	17
AMP PEAK 29(20Q13.2) WILD-TYPE	28	96	28	44	41

Figure S259. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S260. Gene #29: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
AMP PEAK 29(20Q13.2) MUTATED	210	75	57	177	28
AMP PEAK 29(20Q13.2) WILD-TYPE	50	337	36	88	21

Figure S260. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S261. Gene #29: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 29(20Q13.2) MUTATED	83	78	113	29	49
AMP PEAK 29(20Q13.2) WILD-TYPE	49	119	64	59	79

Figure S261. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.11

Table S262. Gene #29: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 29(20Q13.2) MUTATED	101	66	54
AMP PEAK 29(20Q13.2) WILD-TYPE	48	66	63

Figure S262. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.044

Table S263. Gene #29: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 29(20Q13.2) MUTATED	29	44	53	73	22
AMP PEAK 29(20Q13.2) WILD-TYPE	35	62	37	34	9

Figure S263. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S264. Gene #29: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
AMP PEAK 29(20Q13.2) MUTATED	309	172	63
AMP PEAK 29(20Q13.2) WILD-TYPE	234	126	169

Figure S264. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S265. Gene #29: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
AMP PEAK 29(20Q13.2) MUTATED	153	120	104	36	98	33
AMP PEAK 29(20Q13.2) WILD-TYPE	66	44	202	105	85	27

Figure S265. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S266. Gene #29: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
AMP PEAK 29(20Q13.2) MUTATED	211	83	245
AMP PEAK 29(20Q13.2) WILD-TYPE	120	170	231

Figure S266. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S267. Gene #29: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
AMP PEAK 29(20Q13.2) MUTATED	156	104	101	65	42	71
AMP PEAK 29(20Q13.2) WILD-TYPE	75	56	221	62	44	63

Figure S267. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S268. Gene #29: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
AMP PEAK 29(20Q13.2) MUTATED	117	87	42	45	51
AMP PEAK 29(20Q13.2) WILD-TYPE	63	52	57	66	82

Figure S268. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S269. Gene #29: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
AMP PEAK 29(20Q13.2) MUTATED	188	103	51
AMP PEAK 29(20Q13.2) WILD-TYPE	117	144	59

Figure S269. Get High-res Image Gene #29: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S270. Gene #30: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 1(1P36.13) MUTATED	9	11	61	42	31	46	7	12
DEL PEAK 1(1P36.13) WILD-TYPE	12	25	58	54	78	26	13	28

Figure S270. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S271. Gene #30: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 1(1P36.13) MUTATED	57	39	67	39	17
DEL PEAK 1(1P36.13) WILD-TYPE	44	113	47	49	41

Figure S271. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S272. Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 1(1P36.13) MUTATED	168	66	60	135	22
DEL PEAK 1(1P36.13) WILD-TYPE	92	346	33	130	27

Figure S272. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S273. Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 1(1P36.13) MUTATED	58	64	110	24	36
DEL PEAK 1(1P36.13) WILD-TYPE	74	133	67	64	92

Figure S273. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S274. Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 1(1P36.13) MUTATED	263	127	58
DEL PEAK 1(1P36.13) WILD-TYPE	280	171	174

Figure S274. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S275. Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 1(1P36.13) MUTATED	112	106	99	33	80	18
DEL PEAK 1(1P36.13) WILD-TYPE	107	58	207	108	103	42

Figure S275. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S276. Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 1(1P36.13) MUTATED	162	80	195
DEL PEAK 1(1P36.13) WILD-TYPE	169	173	281

Figure S276. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S277. Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 1(1P36.13) MUTATED	116	75	92	60	34	60
DEL PEAK 1(1P36.13) WILD-TYPE	115	85	230	67	52	74

Figure S277. Get High-res Image Gene #30: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S278. Gene #31: 'del_1p22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 2(1P22.1) MUTATED	49	40	62	18	14
DEL PEAK 2(1P22.1) WILD-TYPE	52	112	52	70	44

Figure S278. Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S279. Gene #31: 'del_1p22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 2(1P22.1) MUTATED	143	64	58	81	15
DEL PEAK 2(1P22.1) WILD-TYPE	117	348	35	184	34

Figure S279. Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S280. Gene #31: 'del_1p22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 2(1P22.1) MUTATED	32	55	87	25	29
DEL PEAK 2(1P22.1) WILD-TYPE	100	142	90	63	99

Figure S280. Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S281. Gene #31: 'del_1p22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 2(1P22.1) MUTATED	222	80	56
DEL PEAK 2(1P22.1) WILD-TYPE	321	218	176

Figure S281. Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S282. Gene #31: 'del_1p22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 2(1P22.1) MUTATED	89	96	86	32	38	17
DEL PEAK 2(1P22.1) WILD-TYPE	130	68	220	109	145	43

Figure S282. Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S283. Gene #31: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 2(1P22.1) MUTATED	99	56	84	58	29	26
DEL PEAK 2(1P22.1) WILD-TYPE	132	104	238	69	57	108

Figure S283. Get High-res Image Gene #31: 'del_1p22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S284. Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 3(2Q37.3) MUTATED	5	9	42	49	24	28	6	0
DEL PEAK 3(2Q37.3) WILD-TYPE	16	27	77	47	85	44	14	40

Figure S284. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S285. Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 3(2Q37.3) MUTATED	40	22	48	43	10
DEL PEAK 3(2Q37.3) WILD-TYPE	61	130	66	45	48

Figure S285. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S286. Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 3(2Q37.3) MUTATED	99	43	28	128	18
DEL PEAK 3(2Q37.3) WILD-TYPE	161	369	65	137	31

Figure S286. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S287. Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 3(2Q37.3) MUTATED	64	46	49	15	19
DEL PEAK 3(2Q37.3) WILD-TYPE	68	151	128	73	109

Figure S287. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S288. Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 3(2Q37.3) MUTATED	73	40	14
DEL PEAK 3(2Q37.3) WILD-TYPE	76	92	103

Figure S288. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S289. Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 3(2Q37.3) MUTATED	19	10	41	45	12
DEL PEAK 3(2Q37.3) WILD-TYPE	45	96	49	62	19

Figure S289. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S290. Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 3(2Q37.3) MUTATED	157	132	24
DEL PEAK 3(2Q37.3) WILD-TYPE	386	166	208

Figure S290. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S291. Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 3(2Q37.3) MUTATED	76	72	44	19	88	14
DEL PEAK 3(2Q37.3) WILD-TYPE	143	92	262	122	95	46

Figure S291. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S292. Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 3(2Q37.3) MUTATED	147	40	121
DEL PEAK 3(2Q37.3) WILD-TYPE	184	213	355

Figure S292. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S293. Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 3(2Q37.3) MUTATED	74	53	52	36	25	68
DEL PEAK 3(2Q37.3) WILD-TYPE	157	107	270	91	61	66

Figure S293. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S294. Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 3(2Q37.3) MUTATED	59	61	14	20	27
DEL PEAK 3(2Q37.3) WILD-TYPE	121	78	85	91	106

Figure S294. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S295. Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 3(2Q37.3) MUTATED	108	48	25
DEL PEAK 3(2Q37.3) WILD-TYPE	197	199	85

Figure S295. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S296. Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 4(3P21.31) MUTATED	5	15	38	52	8	35	9	7
DEL PEAK 4(3P21.31) WILD-TYPE	16	21	81	44	101	37	11	33

Figure S296. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S297. Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 4(3P21.31) MUTATED	29	36	55	48	1
DEL PEAK 4(3P21.31) WILD-TYPE	72	116	59	40	57

Figure S297. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S298. Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 4(3P21.31) MUTATED	99	60	18	164	6
DEL PEAK 4(3P21.31) WILD-TYPE	161	352	75	101	43

Figure S298. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S299. Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 4(3P21.31) MUTATED	70	31	74	23	27
DEL PEAK 4(3P21.31) WILD-TYPE	62	166	103	65	101

Figure S299. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S300. Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 4(3P21.31) MUTATED	81	27	36
DEL PEAK 4(3P21.31) WILD-TYPE	68	105	81

Figure S300. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S301. Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 4(3P21.31) MUTATED	5	32	55	41	11
DEL PEAK 4(3P21.31) WILD-TYPE	59	74	35	66	20

Figure S301. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S302. Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 4(3P21.31) MUTATED	144	158	44
DEL PEAK 4(3P21.31) WILD-TYPE	399	140	188

Figure S302. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S303. Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 4(3P21.31) MUTATED	60	85	72	7	100	22
DEL PEAK 4(3P21.31) WILD-TYPE	159	79	234	134	83	38

Figure S303. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S304. Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 4(3P21.31) MUTATED	171	54	115
DEL PEAK 4(3P21.31) WILD-TYPE	160	199	361

Figure S304. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S305. Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 4(3P21.31) MUTATED	98	69	66	23	11	73
DEL PEAK 4(3P21.31) WILD-TYPE	133	91	256	104	75	61

Figure S305. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S306. Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 4(3P21.31) MUTATED	54	80	22	21	36
DEL PEAK 4(3P21.31) WILD-TYPE	126	59	77	90	97

Figure S306. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.031

Table S307. Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 4(3P21.31) MUTATED	123	67	23
DEL PEAK 4(3P21.31) WILD-TYPE	182	180	87

Figure S307. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S308. Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 5(4P16.3) MUTATED	3	10	25	58	22	38	7	6
DEL PEAK 5(4P16.3) WILD-TYPE	18	26	94	38	87	34	13	34

Figure S308. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S309. Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 5(4P16.3) MUTATED	27	28	51	52	11
DEL PEAK 5(4P16.3) WILD-TYPE	74	124	63	36	47

Figure S309. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S310. Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 5(4P16.3) MUTATED	75	50	44	156	14
DEL PEAK 5(4P16.3) WILD-TYPE	185	362	49	109	35

Figure S310. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S311. Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 5(4P16.3) MUTATED	84	40	50	15	29
DEL PEAK 5(4P16.3) WILD-TYPE	48	157	127	73	99

Figure S311. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S312. Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 5(4P16.3) MUTATED	77	38	25
DEL PEAK 5(4P16.3) WILD-TYPE	72	94	92

Figure S312. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S313. Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 5(4P16.3) MUTATED	18	25	54	32	11
DEL PEAK 5(4P16.3) WILD-TYPE	46	81	36	75	20

Figure S313. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S314. Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 5(4P16.3) MUTATED	137	169	31
DEL PEAK 5(4P16.3) WILD-TYPE	406	129	201

Figure S314. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S315. Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 5(4P16.3) MUTATED	49	67	57	24	112	28
DEL PEAK 5(4P16.3) WILD-TYPE	170	97	249	117	71	32

Figure S315. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S316. Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 5(4P16.3) MUTATED	167	47	114
DEL PEAK 5(4P16.3) WILD-TYPE	164	206	362

Figure S316. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S317. Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 5(4P16.3) MUTATED	70	67	53	38	16	84
DEL PEAK 5(4P16.3) WILD-TYPE	161	93	269	89	70	50

Figure S317. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S318. Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 5(4P16.3) MUTATED	48	83	21	27	23
DEL PEAK 5(4P16.3) WILD-TYPE	132	56	78	84	110

Figure S318. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.055

Table S319. Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 5(4P16.3) MUTATED	115	54	33
DEL PEAK 5(4P16.3) WILD-TYPE	190	193	77

Figure S319. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S320. Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 6(4Q35.1) MUTATED	6	9	25	54	24	34	9	9
DEL PEAK 6(4Q35.1) WILD-TYPE	15	27	94	42	85	38	11	31

Figure S320. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S321. Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 6(4Q35.1) MUTATED	25	31	52	49	13
DEL PEAK 6(4Q35.1) WILD-TYPE	76	121	62	39	45

Figure S321. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S322. Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 6(4Q35.1) MUTATED	65	53	49	164	14
DEL PEAK 6(4Q35.1) WILD-TYPE	195	359	44	101	35

Figure S322. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S323. Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 6(4Q35.1) MUTATED	82	38	41	19	38
DEL PEAK 6(4Q35.1) WILD-TYPE	50	159	136	69	90

Figure S323. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S324. Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 6(4Q35.1) MUTATED	80	33	27
DEL PEAK 6(4Q35.1) WILD-TYPE	69	99	90

Figure S324. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q35.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S325. Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 6(4Q35.1) MUTATED	15	26	54	34	11
DEL PEAK 6(4Q35.1) WILD-TYPE	49	80	36	73	20

Figure S325. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S326. Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 6(4Q35.1) MUTATED	146	166	31
DEL PEAK 6(4Q35.1) WILD-TYPE	397	132	201

Figure S326. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S327. Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 6(4Q35.1) MUTATED	44	68	65	27	116	23
DEL PEAK 6(4Q35.1) WILD-TYPE	175	96	241	114	67	37

Figure S327. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S328. Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 6(4Q35.1) MUTATED	167	52	114
DEL PEAK 6(4Q35.1) WILD-TYPE	164	201	362

Figure S328. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S329. Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 6(4Q35.1) MUTATED	65	69	54	43	15	87
DEL PEAK 6(4Q35.1) WILD-TYPE	166	91	268	84	71	47

Figure S329. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S330. Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 6(4Q35.1) MUTATED	50	86	23	26	22
DEL PEAK 6(4Q35.1) WILD-TYPE	130	53	76	85	111

Figure S330. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.13

Table S331. Gene #35: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 6(4Q35.1) MUTATED	116	57	34
DEL PEAK 6(4Q35.1) WILD-TYPE	189	190	76

Figure S331. Get High-res Image Gene #35: 'del_4q35.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S332. Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 7(5Q11.2) MUTATED	3	5	19	69	7	26	3	4
DEL PEAK 7(5Q11.2) WILD-TYPE	18	31	100	27	102	46	17	36

Figure S332. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S333. Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 7(5Q11.2) MUTATED	18	15	38	63	2
DEL PEAK 7(5Q11.2) WILD-TYPE	83	137	76	25	56

Figure S333. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S334. Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 7(5Q11.2) MUTATED	39	32	8	189	12
DEL PEAK 7(5Q11.2) WILD-TYPE	221	380	85	76	37

Figure S334. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S335. Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 7(5Q11.2) MUTATED	99	16	30	9	32
DEL PEAK 7(5Q11.2) WILD-TYPE	33	181	147	79	96

Figure S335. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S336. Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 7(5Q11.2) MUTATED	80	12	23
DEL PEAK 7(5Q11.2) WILD-TYPE	69	120	94

Figure S336. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S337. Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 7(5Q11.2) MUTATED	4	14	64	23	10
DEL PEAK 7(5Q11.2) WILD-TYPE	60	92	26	84	21

Figure S337. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S338. Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 7(5Q11.2) MUTATED	81	181	16
DEL PEAK 7(5Q11.2) WILD-TYPE	462	117	216

Figure S338. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S339. Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 7(5Q11.2) MUTATED	35	44	31	5	137	26
DEL PEAK 7(5Q11.2) WILD-TYPE	184	120	275	136	46	34

Figure S339. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S340. Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 7(5Q11.2) MUTATED	184	29	55
DEL PEAK 7(5Q11.2) WILD-TYPE	147	224	421

Figure S340. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S341. Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 7(5Q11.2) MUTATED	53	64	26	11	8	106
DEL PEAK 7(5Q11.2) WILD-TYPE	178	96	296	116	78	28

Figure S341. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S342. Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 7(5Q11.2) MUTATED	26	98	12	15	20
DEL PEAK 7(5Q11.2) WILD-TYPE	154	41	87	96	113

Figure S342. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S343. Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 7(5Q11.2) MUTATED	125	31	15
DEL PEAK 7(5Q11.2) WILD-TYPE	180	216	95

Figure S343. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S344. Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 8(5Q21.3) MUTATED	2	5	19	71	7	24	5	2
DEL PEAK 8(5Q21.3) WILD-TYPE	19	31	100	25	102	48	15	38

Figure S344. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S345. Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 8(5Q21.3) MUTATED	18	13	36	66	2
DEL PEAK 8(5Q21.3) WILD-TYPE	83	139	78	22	56

Figure S345. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S346. Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 8(5Q21.3) MUTATED	38	23	8	193	10
DEL PEAK 8(5Q21.3) WILD-TYPE	222	389	85	72	39

Figure S346. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S347. Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 8(5Q21.3) MUTATED	106	10	28	6	30
DEL PEAK 8(5Q21.3) WILD-TYPE	26	187	149	82	98

Figure S347. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S348. Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 8(5Q21.3) MUTATED	78	12	23
DEL PEAK 8(5Q21.3) WILD-TYPE	71	120	94

Figure S348. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S349. Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 8(5Q21.3) MUTATED	5	16	62	21	9
DEL PEAK 8(5Q21.3) WILD-TYPE	59	90	28	86	22

Figure S349. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S350. Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 8(5Q21.3) MUTATED	71	188	11
DEL PEAK 8(5Q21.3) WILD-TYPE	472	110	221

Figure S350. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S351. Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 8(5Q21.3) MUTATED	31	40	29	4	142	24
DEL PEAK 8(5Q21.3) WILD-TYPE	188	124	277	137	41	36

Figure S351. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S352. Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 8(5Q21.3) MUTATED	186	24	52
DEL PEAK 8(5Q21.3) WILD-TYPE	145	229	424

Figure S352. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S353. Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 8(5Q21.3) MUTATED	52	67	20	8	6	109
DEL PEAK 8(5Q21.3) WILD-TYPE	179	93	302	119	80	25

Figure S353. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S354. Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 8(5Q21.3) MUTATED	22	101	12	12	18
DEL PEAK 8(5Q21.3) WILD-TYPE	158	38	87	99	115

Figure S354. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S355. Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 8(5Q21.3) MUTATED	124	30	11
DEL PEAK 8(5Q21.3) WILD-TYPE	181	217	99

Figure S355. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S356. Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 9(6P25.3) MUTATED	78	42	17	57	10
DEL PEAK 9(6P25.3) WILD-TYPE	182	370	76	208	39

Figure S356. Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.063

Table S357. Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 9(6P25.3) MUTATED	118	61	24
DEL PEAK 9(6P25.3) WILD-TYPE	425	237	208

Figure S357. Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S358. Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 10(6Q15) MUTATED	6	13	63	20	24	29	4	16
DEL PEAK 10(6Q15) WILD-TYPE	15	23	56	76	85	43	16	24

Figure S358. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.063

Table S359. Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 10(6Q15) MUTATED	50	51	42	18	14
DEL PEAK 10(6Q15) WILD-TYPE	51	101	72	70	44

Figure S359. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S360. Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 10(6Q15) MUTATED	161	91	27	53	26
DEL PEAK 10(6Q15) WILD-TYPE	99	321	66	212	23

Figure S360. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S361. Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 10(6Q15) MUTATED	26	81	73	21	25
DEL PEAK 10(6Q15) WILD-TYPE	106	116	104	67	103

Figure S361. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S362. Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 10(6Q15) MUTATED	221	68	66
DEL PEAK 10(6Q15) WILD-TYPE	322	230	166

Figure S362. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S363. Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 10(6Q15) MUTATED	109	65	94	37	30	20
DEL PEAK 10(6Q15) WILD-TYPE	110	99	212	104	153	40

Figure S363. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S364. Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 10(6Q15) MUTATED	90	49	100	50	43	23
DEL PEAK 10(6Q15) WILD-TYPE	141	111	222	77	43	111

Figure S364. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.031

Table S365. Gene #39: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 10(6Q15) MUTATED	76	25	33	38	47
DEL PEAK 10(6Q15) WILD-TYPE	104	114	66	73	86

Figure S365. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S366. Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 11(6Q27) MUTATED	135	97	26	89	28
DEL PEAK 11(6Q27) WILD-TYPE	125	315	67	176	21

Figure S366. Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.17

Table S367. Gene #40: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 11(6Q27) MUTATED	91	59	100	30	63	28
DEL PEAK 11(6Q27) WILD-TYPE	128	105	206	111	120	32

Figure S367. Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S368. Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 12(7P22.3) MUTATED	4	3	24	25	2	12	2	4
DEL PEAK 12(7P22.3) WILD-TYPE	17	33	95	71	107	60	18	36

Figure S368. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S369. Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 12(7P22.3) MUTATED	20	8	22	24	2
DEL PEAK 12(7P22.3) WILD-TYPE	81	144	92	64	56

Figure S369. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S370. Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 12(7P22.3) MUTATED	53	12	3	65	3
DEL PEAK 12(7P22.3) WILD-TYPE	207	400	90	200	46

Figure S370. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S371. Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 12(7P22.3) MUTATED	30	12	25	6	4
DEL PEAK 12(7P22.3) WILD-TYPE	102	185	152	82	124

Figure S371. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S372. Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 12(7P22.3) MUTATED	63	67	4
DEL PEAK 12(7P22.3) WILD-TYPE	480	231	228

Figure S372. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S373. Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 12(7P22.3) MUTATED	32	28	13	8	48	5
DEL PEAK 12(7P22.3) WILD-TYPE	187	136	293	133	135	55

Figure S373. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S374. Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 12(7P22.3) MUTATED	71	7	54
DEL PEAK 12(7P22.3) WILD-TYPE	260	246	422

Figure S374. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S375. Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 12(7P22.3) MUTATED	42	24	5	14	8	39
DEL PEAK 12(7P22.3) WILD-TYPE	189	136	317	113	78	95

Figure S375. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S376. Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 12(7P22.3) MUTATED	18	34	6	6	11
DEL PEAK 12(7P22.3) WILD-TYPE	162	105	93	105	122

Figure S376. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S377. Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 12(7P22.3) MUTATED	53	16	6
DEL PEAK 12(7P22.3) WILD-TYPE	252	231	104

Figure S377. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S378. Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 13(7Q36.1) MUTATED	16	17	45	17	7
DEL PEAK 13(7Q36.1) WILD-TYPE	85	135	69	71	51

Figure S378. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S379. Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 13(7Q36.1) MUTATED	66	38	14	74	7
DEL PEAK 13(7Q36.1) WILD-TYPE	194	374	79	191	42

Figure S379. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S380. Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 13(7Q36.1) MUTATED	100	77	20
DEL PEAK 13(7Q36.1) WILD-TYPE	443	221	212

Figure S380. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S381. Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 13(7Q36.1) MUTATED	44	46	33	16	40	18
DEL PEAK 13(7Q36.1) WILD-TYPE	175	118	273	125	143	42

Figure S381. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S382. Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 13(7Q36.1) MUTATED	92	20	82
DEL PEAK 13(7Q36.1) WILD-TYPE	239	233	394

Figure S382. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S383. Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 13(7Q36.1) MUTATED	54	46	24	24	15	31
DEL PEAK 13(7Q36.1) WILD-TYPE	177	114	298	103	71	103

Figure S383. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S384. Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 13(7Q36.1) MUTATED	41	39	9	11	17
DEL PEAK 13(7Q36.1) WILD-TYPE	139	100	90	100	116

Figure S384. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S385. Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 13(7Q36.1) MUTATED	76	21	20
DEL PEAK 13(7Q36.1) WILD-TYPE	229	226	90

Figure S385. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S386. Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 14(8P23.2) MUTATED	12	15	78	64	29	47	13	18
DEL PEAK 14(8P23.2) WILD-TYPE	9	21	41	32	80	25	7	22

Figure S386. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S387. Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 14(8P23.2) MUTATED	67	59	78	57	15
DEL PEAK 14(8P23.2) WILD-TYPE	34	93	36	31	43

Figure S387. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S388. Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 14(8P23.2) MUTATED	175	133	22	187	40
DEL PEAK 14(8P23.2) WILD-TYPE	85	279	71	78	9

Figure S388. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S389. Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 14(8P23.2) MUTATED	87	81	102	26	63
DEL PEAK 14(8P23.2) WILD-TYPE	45	116	75	62	65

Figure S389. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.13

Table S390. Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 14(8P23.2) MUTATED	22	57	58	66	22
DEL PEAK 14(8P23.2) WILD-TYPE	42	49	32	41	9

Figure S390. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S391. Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 14(8P23.2) MUTATED	283	193	77
DEL PEAK 14(8P23.2) WILD-TYPE	260	105	155

Figure S391. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S392. Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 14(8P23.2) MUTATED	138	110	122	23	113	47
DEL PEAK 14(8P23.2) WILD-TYPE	81	54	184	118	70	13

Figure S392. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S393. Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 14(8P23.2) MUTATED	215	104	226
DEL PEAK 14(8P23.2) WILD-TYPE	116	149	250

Figure S393. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S394. Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 14(8P23.2) MUTATED	131	110	127	51	43	83
DEL PEAK 14(8P23.2) WILD-TYPE	100	50	195	76	43	51

Figure S394. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S395. Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 14(8P23.2) MUTATED	100	92	43	39	58
DEL PEAK 14(8P23.2) WILD-TYPE	80	47	56	72	75

Figure S395. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S396. Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 14(8P23.2) MUTATED	187	105	40
DEL PEAK 14(8P23.2) WILD-TYPE	118	142	70

Figure S396. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'MRNA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.015

Table S397. Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 15(8P11.21) MUTATED	4	3	22	24	8	26	7	7
DEL PEAK 15(8P11.21) WILD-TYPE	17	33	97	72	101	46	13	33

Figure S397. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.027

Table S398. Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 15(8P11.21) MUTATED	20	18	37	21	5
DEL PEAK 15(8P11.21) WILD-TYPE	81	134	77	67	53

Figure S398. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S399. Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 15(8P11.21) MUTATED	56	44	14	85	1
DEL PEAK 15(8P11.21) WILD-TYPE	204	368	79	180	48

Figure S399. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.029

Table S400. Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 15(8P11.21) MUTATED	5	21	21	23	16
DEL PEAK 15(8P11.21) WILD-TYPE	59	85	69	84	15

Figure S400. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S401. Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 15(8P11.21) MUTATED	97	78	25
DEL PEAK 15(8P11.21) WILD-TYPE	446	220	207

Figure S401. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S402. Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 15(8P11.21) MUTATED	37	54	38	10	35	26
DEL PEAK 15(8P11.21) WILD-TYPE	182	110	268	131	148	34

Figure S402. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S403. Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 15(8P11.21) MUTATED	87	27	84
DEL PEAK 15(8P11.21) WILD-TYPE	244	226	392

Figure S403. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S404. Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 15(8P11.21) MUTATED	52	61	29	23	11	22
DEL PEAK 15(8P11.21) WILD-TYPE	179	99	293	104	75	112

Figure S404. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.098

Table S405. Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 15(8P11.21) MUTATED	77	31	17
DEL PEAK 15(8P11.21) WILD-TYPE	228	216	93

Figure S405. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S406. Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 16(9P23) MUTATED	9	15	57	21	22	34	10	5
DEL PEAK 16(9P23) WILD-TYPE	12	21	62	75	87	38	10	35

Figure S406. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S407. Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 16(9P23) MUTATED	49	36	61	17	10
DEL PEAK 16(9P23) WILD-TYPE	52	116	53	71	48

Figure S407. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S408. Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 16(9P23) MUTATED	159	46	15	93	11
DEL PEAK 16(9P23) WILD-TYPE	101	366	78	172	38

Figure S408. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S409. Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 16(9P23) MUTATED	37	43	90	14	25
DEL PEAK 16(9P23) WILD-TYPE	95	154	87	74	103

Figure S409. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.16

Table S410. Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 16(9P23) MUTATED	15	31	26	53	15
DEL PEAK 16(9P23) WILD-TYPE	49	75	64	54	16

Figure S410. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S411. Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 16(9P23) MUTATED	200	90	34
DEL PEAK 16(9P23) WILD-TYPE	343	208	198

Figure S411. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S412. Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 16(9P23) MUTATED	101	84	60	16	35	28
DEL PEAK 16(9P23) WILD-TYPE	118	80	246	125	148	32

Figure S412. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S413. Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 16(9P23) MUTATED	124	41	152
DEL PEAK 16(9P23) WILD-TYPE	207	212	324

Figure S413. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S414. Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 16(9P23) MUTATED	104	76	54	37	24	22
DEL PEAK 16(9P23) WILD-TYPE	127	84	268	90	62	112

Figure S414. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S415. Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 16(9P23) MUTATED	74	39	23	20	33
DEL PEAK 16(9P23) WILD-TYPE	106	100	76	91	100

Figure S415. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S416. Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 16(9P23) MUTATED	112	56	21
DEL PEAK 16(9P23) WILD-TYPE	193	191	89

Figure S416. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S417. Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 17(9P21.3) MUTATED	9	12	62	33	24	38	8	6
DEL PEAK 17(9P21.3) WILD-TYPE	12	24	57	63	85	34	12	34

Figure S417. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S418. Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 17(9P21.3) MUTATED	53	34	65	28	12
DEL PEAK 17(9P21.3) WILD-TYPE	48	118	49	60	46

Figure S418. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S419. Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 17(9P21.3) MUTATED	164	52	18	117	12
DEL PEAK 17(9P21.3) WILD-TYPE	96	360	75	148	37

Figure S419. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S420. Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 17(9P21.3) MUTATED	51	49	86	14	28
DEL PEAK 17(9P21.3) WILD-TYPE	81	148	91	74	100

Figure S420. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S421. Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 17(9P21.3) MUTATED	210	117	33
DEL PEAK 17(9P21.3) WILD-TYPE	333	181	199

Figure S421. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S422. Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 17(9P21.3) MUTATED	104	89	56	21	60	30
DEL PEAK 17(9P21.3) WILD-TYPE	115	75	250	120	123	30

Figure S422. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S423. Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 17(9P21.3) MUTATED	146	45	162
DEL PEAK 17(9P21.3) WILD-TYPE	185	208	314

Figure S423. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S424. Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 17(9P21.3) MUTATED	108	84	53	41	28	39
DEL PEAK 17(9P21.3) WILD-TYPE	123	76	269	86	58	95

Figure S424. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.017

Table S425. Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 17(9P21.3) MUTATED	76	54	24	25	30
DEL PEAK 17(9P21.3) WILD-TYPE	104	85	75	86	103

Figure S425. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S426. Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 17(9P21.3) MUTATED	128	58	23
DEL PEAK 17(9P21.3) WILD-TYPE	177	189	87

Figure S426. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.19

Table S427. Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 18(9Q21.11) MUTATED	5	6	42	41	24	27	7	5
DEL PEAK 18(9Q21.11) WILD-TYPE	16	30	77	55	85	45	13	35

Figure S427. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S428. Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 18(9Q21.11) MUTATED	37	25	50	35	10
DEL PEAK 18(9Q21.11) WILD-TYPE	64	127	64	53	48

Figure S428. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S429. Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 18(9Q21.11) MUTATED	110	43	18	108	14
DEL PEAK 18(9Q21.11) WILD-TYPE	150	369	75	157	35

Figure S429. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S430. Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 18(9Q21.11) MUTATED	55	40	54	12	26
DEL PEAK 18(9Q21.11) WILD-TYPE	77	157	123	76	102

Figure S430. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S431. Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 18(9Q21.11) MUTATED	69	33	22
DEL PEAK 18(9Q21.11) WILD-TYPE	80	99	95

Figure S431. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S432. Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 18(9Q21.11) MUTATED	158	107	28
DEL PEAK 18(9Q21.11) WILD-TYPE	385	191	204

Figure S432. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S433. Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 18(9Q21.11) MUTATED	79	60	48	15	69	22
DEL PEAK 18(9Q21.11) WILD-TYPE	140	104	258	126	114	38

Figure S433. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S434. Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 18(9Q21.11) MUTATED	139	33	114
DEL PEAK 18(9Q21.11) WILD-TYPE	192	220	362

Figure S434. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S435. Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 18(9Q21.11) MUTATED	77	67	38	30	19	55
DEL PEAK 18(9Q21.11) WILD-TYPE	154	93	284	97	67	79

Figure S435. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S436. Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 18(9Q21.11) MUTATED	55	56	21	15	22
DEL PEAK 18(9Q21.11) WILD-TYPE	125	83	78	96	111

Figure S436. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S437. Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 18(9Q21.11) MUTATED	107	45	17
DEL PEAK 18(9Q21.11) WILD-TYPE	198	202	93

Figure S437. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S438. Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 19(9Q34.2) MUTATED	6	4	40	55	23	18	7	4
DEL PEAK 19(9Q34.2) WILD-TYPE	15	32	79	41	86	54	13	36

Figure S438. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S439. Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 19(9Q34.2) MUTATED	36	23	38	50	10
DEL PEAK 19(9Q34.2) WILD-TYPE	65	129	76	38	48

Figure S439. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S440. Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 19(9Q34.2) MUTATED	98	30	14	140	14
DEL PEAK 19(9Q34.2) WILD-TYPE	162	382	79	125	35

Figure S440. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S441. Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 19(9Q34.2) MUTATED	74	37	47	10	21
DEL PEAK 19(9Q34.2) WILD-TYPE	58	160	130	78	107

Figure S441. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S442. Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 19(9Q34.2) MUTATED	68	33	21
DEL PEAK 19(9Q34.2) WILD-TYPE	81	99	96

Figure S442. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S443. Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 19(9Q34.2) MUTATED	12	20	50	37	3
DEL PEAK 19(9Q34.2) WILD-TYPE	52	86	40	70	28

Figure S443. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S444. Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 19(9Q34.2) MUTATED	144	133	18
DEL PEAK 19(9Q34.2) WILD-TYPE	399	165	214

Figure S444. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S445. Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 19(9Q34.2) MUTATED	75	51	39	14	102	14
DEL PEAK 19(9Q34.2) WILD-TYPE	144	113	267	127	81	46

Figure S445. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S446. Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 19(9Q34.2) MUTATED	155	31	101
DEL PEAK 19(9Q34.2) WILD-TYPE	176	222	375

Figure S446. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S447. Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 19(9Q34.2) MUTATED	69	61	33	29	17	78
DEL PEAK 19(9Q34.2) WILD-TYPE	162	99	289	98	69	56

Figure S447. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S448. Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 19(9Q34.2) MUTATED	48	77	17	13	20
DEL PEAK 19(9Q34.2) WILD-TYPE	132	62	82	98	113

Figure S448. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S449. Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 19(9Q34.2) MUTATED	118	43	14
DEL PEAK 19(9Q34.2) WILD-TYPE	187	204	96

Figure S449. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S450. Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 20(10Q23.31) MUTATED	7	6	36	49	20	21	7	3
DEL PEAK 20(10Q23.31) WILD-TYPE	14	30	83	47	89	51	13	37

Figure S450. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S451. Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 20(10Q23.31) MUTATED	28	29	39	45	8
DEL PEAK 20(10Q23.31) WILD-TYPE	73	123	75	43	50

Figure S451. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S452. Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 20(10Q23.31) MUTATED	88	53	24	137	18
DEL PEAK 20(10Q23.31) WILD-TYPE	172	359	69	128	31

Figure S452. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S453. Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 20(10Q23.31) MUTATED	76	40	65	17	26
DEL PEAK 20(10Q23.31) WILD-TYPE	56	157	112	71	102

Figure S453. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S454. Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 20(10Q23.31) MUTATED	68	30	20
DEL PEAK 20(10Q23.31) WILD-TYPE	81	102	97

Figure S454. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S455. Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 20(10Q23.31) MUTATED	12	17	45	34	10
DEL PEAK 20(10Q23.31) WILD-TYPE	52	89	45	73	21

Figure S455. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S456. Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 20(10Q23.31) MUTATED	145	142	31
DEL PEAK 20(10Q23.31) WILD-TYPE	398	156	201

Figure S456. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S457. Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 20(10Q23.31) MUTATED	69	65	49	17	96	22
DEL PEAK 20(10Q23.31) WILD-TYPE	150	99	257	124	87	38

Figure S457. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S458. Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 20(10Q23.31) MUTATED	144	56	111
DEL PEAK 20(10Q23.31) WILD-TYPE	187	197	365

Figure S458. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S459. Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 20(10Q23.31) MUTATED	66	71	57	26	18	73
DEL PEAK 20(10Q23.31) WILD-TYPE	165	89	265	101	68	61

Figure S459. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S460. Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 20(10Q23.31) MUTATED	53	74	22	17	32
DEL PEAK 20(10Q23.31) WILD-TYPE	127	65	77	94	101

Figure S460. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S461. Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 20(10Q23.31) MUTATED	116	61	21
DEL PEAK 20(10Q23.31) WILD-TYPE	189	186	89

Figure S461. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S462. Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 21(10Q26.3) MUTATED	8	7	38	55	14	22	6	4
DEL PEAK 21(10Q26.3) WILD-TYPE	13	29	81	41	95	50	14	36

Figure S462. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S463. Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 21(10Q26.3) MUTATED	31	23	44	49	7
DEL PEAK 21(10Q26.3) WILD-TYPE	70	129	70	39	51

Figure S463. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S464. Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 21(10Q26.3) MUTATED	95	50	21	140	13
DEL PEAK 21(10Q26.3) WILD-TYPE	165	362	72	125	36

Figure S464. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S465. Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 21(10Q26.3) MUTATED	75	37	68	12	24
DEL PEAK 21(10Q26.3) WILD-TYPE	57	160	109	76	104

Figure S465. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S466. Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 21(10Q26.3) MUTATED	73	28	24
DEL PEAK 21(10Q26.3) WILD-TYPE	76	104	93

Figure S466. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S467. Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 21(10Q26.3) MUTATED	11	16	48	36	14
DEL PEAK 21(10Q26.3) WILD-TYPE	53	90	42	71	17

Figure S467. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S468. Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 21(10Q26.3) MUTATED	145	150	23
DEL PEAK 21(10Q26.3) WILD-TYPE	398	148	209

Figure S468. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S469. Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 21(10Q26.3) MUTATED	64	71	43	16	98	26
DEL PEAK 21(10Q26.3) WILD-TYPE	155	93	263	125	85	34

Figure S469. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S470. Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 21(10Q26.3) MUTATED	147	48	113
DEL PEAK 21(10Q26.3) WILD-TYPE	184	205	363

Figure S470. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S471. Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 21(10Q26.3) MUTATED	76	73	48	21	18	72
DEL PEAK 21(10Q26.3) WILD-TYPE	155	87	274	106	68	62

Figure S471. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S472. Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 21(10Q26.3) MUTATED	60	72	20	13	33
DEL PEAK 21(10Q26.3) WILD-TYPE	120	67	79	98	100

Figure S472. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S473. Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 21(10Q26.3) MUTATED	125	54	19
DEL PEAK 21(10Q26.3) WILD-TYPE	180	193	91

Figure S473. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S474. Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 22(11P15.5) MUTATED	3	8	33	48	14	34	7	9
DEL PEAK 22(11P15.5) WILD-TYPE	18	28	86	48	95	38	13	31

Figure S474. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S475. Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 22(11P15.5) MUTATED	24	32	50	42	8
DEL PEAK 22(11P15.5) WILD-TYPE	77	120	64	46	50

Figure S475. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S476. Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 22(11P15.5) MUTATED	89	36	17	159	8
DEL PEAK 22(11P15.5) WILD-TYPE	171	376	76	106	41

Figure S476. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S477. Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 22(11P15.5) MUTATED	69	33	57	15	22
DEL PEAK 22(11P15.5) WILD-TYPE	63	164	120	73	106

Figure S477. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S478. Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 22(11P15.5) MUTATED	77	27	26
DEL PEAK 22(11P15.5) WILD-TYPE	72	105	91

Figure S478. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S479. Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 22(11P15.5) MUTATED	11	20	48	36	15
DEL PEAK 22(11P15.5) WILD-TYPE	53	86	42	71	16

Figure S479. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S480. Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 22(11P15.5) MUTATED	133	147	28
DEL PEAK 22(11P15.5) WILD-TYPE	410	151	204

Figure S480. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S481. Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 22(11P15.5) MUTATED	57	63	54	15	91	28
DEL PEAK 22(11P15.5) WILD-TYPE	162	101	252	126	92	32

Figure S481. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S482. Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 22(11P15.5) MUTATED	157	43	101
DEL PEAK 22(11P15.5) WILD-TYPE	174	210	375

Figure S482. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S483. Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 22(11P15.5) MUTATED	76	68	49	27	12	69
DEL PEAK 22(11P15.5) WILD-TYPE	155	92	273	100	74	65

Figure S483. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S484. Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 22(11P15.5) MUTATED	47	69	20	15	30
DEL PEAK 22(11P15.5) WILD-TYPE	133	70	79	96	103

Figure S484. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S485. Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 22(11P15.5) MUTATED	110	51	20
DEL PEAK 22(11P15.5) WILD-TYPE	195	196	90

Figure S485. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q23.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S486. Gene #52: 'del_11q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 23(11Q23.3) MUTATED	12	21	89	40	36	37	12	22
DEL PEAK 23(11Q23.3) WILD-TYPE	9	15	30	56	73	35	8	18

Figure S486. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q23.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S487. Gene #52: 'del_11q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 23(11Q23.3) MUTATED	77	74	64	37	17
DEL PEAK 23(11Q23.3) WILD-TYPE	24	78	50	51	41

Figure S487. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S488. Gene #52: 'del_11q23.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 23(11Q23.3) MUTATED	212	134	39	140	21
DEL PEAK 23(11Q23.3) WILD-TYPE	48	278	54	125	28

Figure S488. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S489. Gene #52: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 23(11Q23.3) MUTATED	66	98	123	33	44
DEL PEAK 23(11Q23.3) WILD-TYPE	66	99	54	55	84

Figure S489. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.3' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S490. Gene #52: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 23(11Q23.3) MUTATED	20	54	41	75	17
DEL PEAK 23(11Q23.3) WILD-TYPE	44	52	49	32	14

Figure S490. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q23.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S491. Gene #52: 'del_11q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 23(11Q23.3) MUTATED	313	138	93
DEL PEAK 23(11Q23.3) WILD-TYPE	230	160	139

Figure S491. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S492. Gene #52: 'del_11q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 23(11Q23.3) MUTATED	158	100	151	33	78	24
DEL PEAK 23(11Q23.3) WILD-TYPE	61	64	155	108	105	36

Figure S492. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.013

Table S493. Gene #52: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 23(11Q23.3) MUTATED	149	79	139	59	45	60
DEL PEAK 23(11Q23.3) WILD-TYPE	82	81	183	68	41	74

Figure S493. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.042

Table S494. Gene #52: 'del_11q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 23(11Q23.3) MUTATED	106	63	57	37	64
DEL PEAK 23(11Q23.3) WILD-TYPE	74	76	42	74	69

Figure S494. Get High-res Image Gene #52: 'del_11q23.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.025

Table S495. Gene #53: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 24(12P13.1) MUTATED	55	47	14	65	7
DEL PEAK 24(12P13.1) WILD-TYPE	205	365	79	200	42

Figure S495. Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.15

Table S496. Gene #53: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 24(12P13.1) MUTATED	83	73	31
DEL PEAK 24(12P13.1) WILD-TYPE	460	225	201

Figure S496. Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.1

Table S497. Gene #53: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 24(12P13.1) MUTATED	37	36	40	14	42	18
DEL PEAK 24(12P13.1) WILD-TYPE	182	128	266	127	141	42

Figure S497. Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.021

Table S498. Gene #53: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 24(12P13.1) MUTATED	44	46	41	12	14	28
DEL PEAK 24(12P13.1) WILD-TYPE	187	114	281	115	72	106

Figure S498. Get High-res Image Gene #53: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S499. Gene #54: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 25(12Q23.1) MUTATED	2	1	14	43	6	22	4	4
DEL PEAK 25(12Q23.1) WILD-TYPE	19	35	105	53	103	50	16	36

Figure S499. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S500. Gene #54: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 25(12Q23.1) MUTATED	12	10	34	37	3
DEL PEAK 25(12Q23.1) WILD-TYPE	89	142	80	51	55

Figure S500. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S501. Gene #54: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 25(12Q23.1) MUTATED	33	32	16	115	5
DEL PEAK 25(12Q23.1) WILD-TYPE	227	380	77	150	44

Figure S501. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S502. Gene #54: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 25(12Q23.1) MUTATED	68	14	30	12	14
DEL PEAK 25(12Q23.1) WILD-TYPE	64	183	147	76	114

Figure S502. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S503. Gene #54: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 25(12Q23.1) MUTATED	49	11	18
DEL PEAK 25(12Q23.1) WILD-TYPE	100	121	99

Figure S503. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S504. Gene #54: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 25(12Q23.1) MUTATED	5	11	40	15	7
DEL PEAK 25(12Q23.1) WILD-TYPE	59	95	50	92	24

Figure S504. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S505. Gene #54: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 25(12Q23.1) MUTATED	66	114	19
DEL PEAK 25(12Q23.1) WILD-TYPE	477	184	213

Figure S505. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S506. Gene #54: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 25(12Q23.1) MUTATED	26	42	26	7	80	18
DEL PEAK 25(12Q23.1) WILD-TYPE	193	122	280	134	103	42

Figure S506. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S507. Gene #54: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 25(12Q23.1) MUTATED	117	25	55
DEL PEAK 25(12Q23.1) WILD-TYPE	214	228	421

Figure S507. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S508. Gene #54: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 25(12Q23.1) MUTATED	46	45	28	12	7	59
DEL PEAK 25(12Q23.1) WILD-TYPE	185	115	294	115	79	75

Figure S508. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S509. Gene #54: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 25(12Q23.1) MUTATED	27	62	7	14	21
DEL PEAK 25(12Q23.1) WILD-TYPE	153	77	92	97	112

Figure S509. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S510. Gene #54: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 25(12Q23.1) MUTATED	90	30	11
DEL PEAK 25(12Q23.1) WILD-TYPE	215	217	99

Figure S510. Get High-res Image Gene #54: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S511. Gene #55: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 26(12Q24.31) MUTATED	4	6	12	42	6	20	5	6
DEL PEAK 26(12Q24.31) WILD-TYPE	17	30	107	54	103	52	15	34

Figure S511. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S512. Gene #55: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 26(12Q24.31) MUTATED	10	15	35	37	4
DEL PEAK 26(12Q24.31) WILD-TYPE	91	137	79	51	54

Figure S512. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q24.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S513. Gene #55: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 26(12Q24.31) MUTATED	33	40	17	115	6
DEL PEAK 26(12Q24.31) WILD-TYPE	227	372	76	150	43

Figure S513. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S514. Gene #55: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 26(12Q24.31) MUTATED	68	18	26	14	16
DEL PEAK 26(12Q24.31) WILD-TYPE	64	179	151	74	112

Figure S514. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.31' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S515. Gene #55: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 26(12Q24.31) MUTATED	49	13	20
DEL PEAK 26(12Q24.31) WILD-TYPE	100	119	97

Figure S515. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S516. Gene #55: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 26(12Q24.31) MUTATED	7	13	36	16	10
DEL PEAK 26(12Q24.31) WILD-TYPE	57	93	54	91	21

Figure S516. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S517. Gene #55: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 26(12Q24.31) MUTATED	63	118	29
DEL PEAK 26(12Q24.31) WILD-TYPE	480	180	203

Figure S517. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S518. Gene #55: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 26(12Q24.31) MUTATED	25	37	41	6	79	22
DEL PEAK 26(12Q24.31) WILD-TYPE	194	127	265	135	104	38

Figure S518. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S519. Gene #55: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 26(12Q24.31) MUTATED	108	37	63
DEL PEAK 26(12Q24.31) WILD-TYPE	223	216	413

Figure S519. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S520. Gene #55: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 26(12Q24.31) MUTATED	49	44	38	14	5	58
DEL PEAK 26(12Q24.31) WILD-TYPE	182	116	284	113	81	76

Figure S520. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S521. Gene #55: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 26(12Q24.31) MUTATED	29	60	12	16	23
DEL PEAK 26(12Q24.31) WILD-TYPE	151	79	87	95	110

Figure S521. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.023

Table S522. Gene #55: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 26(12Q24.31) MUTATED	88	37	15
DEL PEAK 26(12Q24.31) WILD-TYPE	217	210	95

Figure S522. Get High-res Image Gene #55: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S523. Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 27(13Q14.2) MUTATED	8	12	70	60	34	41	9	13
DEL PEAK 27(13Q14.2) WILD-TYPE	13	24	49	36	75	31	11	27

Figure S523. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S524. Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 27(13Q14.2) MUTATED	64	47	67	56	13
DEL PEAK 27(13Q14.2) WILD-TYPE	37	105	47	32	45

Figure S524. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S525. Gene #56: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 27(13Q14.2) MUTATED	164	90	54	159	27
DEL PEAK 27(13Q14.2) WILD-TYPE	96	322	39	106	22

Figure S525. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S526. Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 27(13Q14.2) MUTATED	84	81	97	24	44
DEL PEAK 27(13Q14.2) WILD-TYPE	48	116	80	64	84

Figure S526. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S527. Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 27(13Q14.2) MUTATED	19	44	58	61	10
DEL PEAK 27(13Q14.2) WILD-TYPE	45	62	32	46	21

Figure S527. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S528. Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 27(13Q14.2) MUTATED	257	172	63
DEL PEAK 27(13Q14.2) WILD-TYPE	286	126	169

Figure S528. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S529. Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 27(13Q14.2) MUTATED	112	96	109	37	114	24
DEL PEAK 27(13Q14.2) WILD-TYPE	107	68	197	104	69	36

Figure S529. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S530. Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 27(13Q14.2) MUTATED	188	83	212
DEL PEAK 27(13Q14.2) WILD-TYPE	143	170	264

Figure S530. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S531. Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 27(13Q14.2) MUTATED	130	72	107	49	37	88
DEL PEAK 27(13Q14.2) WILD-TYPE	101	88	215	78	49	46

Figure S531. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S532. Gene #56: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 27(13Q14.2) MUTATED	92	87	35	25	46
DEL PEAK 27(13Q14.2) WILD-TYPE	88	52	64	86	87

Figure S532. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S533. Gene #56: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 27(13Q14.2) MUTATED	163	84	38
DEL PEAK 27(13Q14.2) WILD-TYPE	142	163	72

Figure S533. Get High-res Image Gene #56: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S534. Gene #57: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 28(14Q24.1) MUTATED	4	7	47	63	10	22	10	8
DEL PEAK 28(14Q24.1) WILD-TYPE	17	29	72	33	99	50	10	32

Figure S534. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S535. Gene #57: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 28(14Q24.1) MUTATED	37	30	41	59	4
DEL PEAK 28(14Q24.1) WILD-TYPE	64	122	73	29	54

Figure S535. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S536. Gene #57: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 28(14Q24.1) MUTATED	96	48	22	170	17
DEL PEAK 28(14Q24.1) WILD-TYPE	164	364	71	95	32

Figure S536. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S537. Gene #57: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 28(14Q24.1) MUTATED	88	38	58	17	31
DEL PEAK 28(14Q24.1) WILD-TYPE	44	159	119	71	97

Figure S537. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q24.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S538. Gene #57: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 28(14Q24.1) MUTATED	77	27	33
DEL PEAK 28(14Q24.1) WILD-TYPE	72	105	84

Figure S538. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S539. Gene #57: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 28(14Q24.1) MUTATED	6	27	58	38	8
DEL PEAK 28(14Q24.1) WILD-TYPE	58	79	32	69	23

Figure S539. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S540. Gene #57: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 28(14Q24.1) MUTATED	151	166	34
DEL PEAK 28(14Q24.1) WILD-TYPE	392	132	198

Figure S540. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S541. Gene #57: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 28(14Q24.1) MUTATED	71	68	57	15	124	16
DEL PEAK 28(14Q24.1) WILD-TYPE	148	96	249	126	59	44

Figure S541. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S542. Gene #57: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 28(14Q24.1) MUTATED	177	50	116
DEL PEAK 28(14Q24.1) WILD-TYPE	154	203	360

Figure S542. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S543. Gene #57: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 28(14Q24.1) MUTATED	82	68	54	26	17	96
DEL PEAK 28(14Q24.1) WILD-TYPE	149	92	268	101	69	38

Figure S543. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S544. Gene #57: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 28(14Q24.1) MUTATED	56	89	19	24	31
DEL PEAK 28(14Q24.1) WILD-TYPE	124	50	80	87	102

Figure S544. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S545. Gene #57: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 28(14Q24.1) MUTATED	145	52	22
DEL PEAK 28(14Q24.1) WILD-TYPE	160	195	88

Figure S545. Get High-res Image Gene #57: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S546. Gene #58: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 29(15Q13.1) MUTATED	5	11	41	58	24	34	10	8
DEL PEAK 29(15Q13.1) WILD-TYPE	16	25	78	38	85	38	10	32

Figure S546. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S547. Gene #58: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 29(15Q13.1) MUTATED	36	35	54	54	12
DEL PEAK 29(15Q13.1) WILD-TYPE	65	117	60	34	46

Figure S547. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S548. Gene #58: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 29(15Q13.1) MUTATED	92	49	44	175	14
DEL PEAK 29(15Q13.1) WILD-TYPE	168	363	49	90	35

Figure S548. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S549. Gene #58: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 29(15Q13.1) MUTATED	86	45	65	20	29
DEL PEAK 29(15Q13.1) WILD-TYPE	46	152	112	68	99

Figure S549. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q13.1' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S550. Gene #58: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 29(15Q13.1) MUTATED	80	39	38
DEL PEAK 29(15Q13.1) WILD-TYPE	69	93	79

Figure S550. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.019

Table S551. Gene #58: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 29(15Q13.1) MUTATED	18	29	54	43	13
DEL PEAK 29(15Q13.1) WILD-TYPE	46	77	36	64	18

Figure S551. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S552. Gene #58: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 29(15Q13.1) MUTATED	175	166	31
DEL PEAK 29(15Q13.1) WILD-TYPE	368	132	201

Figure S552. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S553. Gene #58: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 29(15Q13.1) MUTATED	70	75	62	24	120	21
DEL PEAK 29(15Q13.1) WILD-TYPE	149	89	244	117	63	39

Figure S553. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S554. Gene #58: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 29(15Q13.1) MUTATED	185	45	135
DEL PEAK 29(15Q13.1) WILD-TYPE	146	208	341

Figure S554. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S555. Gene #58: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 29(15Q13.1) MUTATED	89	70	48	46	17	95
DEL PEAK 29(15Q13.1) WILD-TYPE	142	90	274	81	69	39

Figure S555. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S556. Gene #58: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 29(15Q13.1) MUTATED	65	90	21	28	26
DEL PEAK 29(15Q13.1) WILD-TYPE	115	49	78	83	107

Figure S556. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S557. Gene #58: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 29(15Q13.1) MUTATED	139	54	37
DEL PEAK 29(15Q13.1) WILD-TYPE	166	193	73

Figure S557. Get High-res Image Gene #58: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S558. Gene #59: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 30(16Q24.3) MUTATED	16	25	81	27	94	45	13	35
DEL PEAK 30(16Q24.3) WILD-TYPE	5	11	38	69	15	27	7	5

Figure S558. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S559. Gene #59: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 30(16Q24.3) MUTATED	74	124	71	22	45
DEL PEAK 30(16Q24.3) WILD-TYPE	27	28	43	66	13

Figure S559. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S560. Gene #59: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 30(16Q24.3) MUTATED	166	292	75	121	38
DEL PEAK 30(16Q24.3) WILD-TYPE	94	120	18	144	11

Figure S560. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S561. Gene #59: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 30(16Q24.3) MUTATED	53	152	118	61	72
DEL PEAK 30(16Q24.3) WILD-TYPE	79	45	59	27	56

Figure S561. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S562. Gene #59: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 30(16Q24.3) MUTATED	64	103	84
DEL PEAK 30(16Q24.3) WILD-TYPE	85	29	33

Figure S562. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S563. Gene #59: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 30(16Q24.3) MUTATED	54	80	28	74	15
DEL PEAK 30(16Q24.3) WILD-TYPE	10	26	62	33	16

Figure S563. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S564. Gene #59: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 30(16Q24.3) MUTATED	383	119	186
DEL PEAK 30(16Q24.3) WILD-TYPE	160	179	46

Figure S564. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S565. Gene #59: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 30(16Q24.3) MUTATED	156	100	246	98	60	28
DEL PEAK 30(16Q24.3) WILD-TYPE	63	64	60	43	123	32

Figure S565. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S566. Gene #59: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 30(16Q24.3) MUTATED	151	181	348
DEL PEAK 30(16Q24.3) WILD-TYPE	180	72	128

Figure S566. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S567. Gene #59: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 30(16Q24.3) MUTATED	139	78	240	111	62	50
DEL PEAK 30(16Q24.3) WILD-TYPE	92	82	82	16	24	84

Figure S567. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S568. Gene #59: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 30(16Q24.3) MUTATED	119	59	68	78	92
DEL PEAK 30(16Q24.3) WILD-TYPE	61	80	31	33	41

Figure S568. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S569. Gene #59: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 30(16Q24.3) MUTATED	154	177	85
DEL PEAK 30(16Q24.3) WILD-TYPE	151	70	25

Figure S569. Get High-res Image Gene #59: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S570. Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 31(17P12) MUTATED	14	27	78	65	33	62	15	24
DEL PEAK 31(17P12) WILD-TYPE	7	9	41	31	76	10	5	16

Figure S570. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S571. Gene #60: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 31(17P12) MUTATED	69	86	93	58	12
DEL PEAK 31(17P12) WILD-TYPE	32	66	21	30	46

Figure S571. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S572. Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 31(17P12) MUTATED	208	161	42	209	30
DEL PEAK 31(17P12) WILD-TYPE	52	251	51	56	19

Figure S572. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S573. Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 31(17P12) MUTATED	87	98	133	43	65
DEL PEAK 31(17P12) WILD-TYPE	45	99	44	45	63

Figure S573. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S574. Gene #60: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 31(17P12) MUTATED	116	66	66
DEL PEAK 31(17P12) WILD-TYPE	33	66	51

Figure S574. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S575. Gene #60: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 31(17P12) MUTATED	23	57	65	77	26
DEL PEAK 31(17P12) WILD-TYPE	41	49	25	30	5

Figure S575. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S576. Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 31(17P12) MUTATED	316	214	116
DEL PEAK 31(17P12) WILD-TYPE	227	84	116

Figure S576. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S577. Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 31(17P12) MUTATED	146	135	173	28	116	48
DEL PEAK 31(17P12) WILD-TYPE	73	29	133	113	67	12

Figure S577. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S578. Gene #60: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 31(17P12) MUTATED	238	130	271
DEL PEAK 31(17P12) WILD-TYPE	93	123	205

Figure S578. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.008

Table S579. Gene #60: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 31(17P12) MUTATED	160	108	168	70	40	93
DEL PEAK 31(17P12) WILD-TYPE	71	52	154	57	46	41

Figure S579. Get High-res Image Gene #60: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S580. Gene #61: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 32(17Q21.31) MUTATED	7	17	28	53	13	50	9	15
DEL PEAK 32(17Q21.31) WILD-TYPE	14	19	91	43	96	22	11	25

Figure S580. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S581. Gene #61: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 32(17Q21.31) MUTATED	24	49	70	46	3
DEL PEAK 32(17Q21.31) WILD-TYPE	77	103	44	42	55

Figure S581. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S582. Gene #61: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 32(17Q21.31) MUTATED	85	84	23	170	9
DEL PEAK 32(17Q21.31) WILD-TYPE	175	328	70	95	40

Figure S582. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S583. Gene #61: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 32(17Q21.31) MUTATED	81	30	63	18	40
DEL PEAK 32(17Q21.31) WILD-TYPE	51	167	114	70	88

Figure S583. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S584. Gene #61: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 32(17Q21.31) MUTATED	90	24	44
DEL PEAK 32(17Q21.31) WILD-TYPE	59	108	73

Figure S584. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S585. Gene #61: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 32(17Q21.31) MUTATED	10	34	52	36	26
DEL PEAK 32(17Q21.31) WILD-TYPE	54	72	38	71	5

Figure S585. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S586. Gene #61: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 32(17Q21.31) MUTATED	142	174	54
DEL PEAK 32(17Q21.31) WILD-TYPE	401	124	178

Figure S586. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S587. Gene #61: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 32(17Q21.31) MUTATED	46	91	89	9	96	39
DEL PEAK 32(17Q21.31) WILD-TYPE	173	73	217	132	87	21

Figure S587. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S588. Gene #61: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 32(17Q21.31) MUTATED	177	61	125
DEL PEAK 32(17Q21.31) WILD-TYPE	154	192	351

Figure S588. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S589. Gene #61: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 32(17Q21.31) MUTATED	103	70	68	32	11	79
DEL PEAK 32(17Q21.31) WILD-TYPE	128	90	254	95	75	55

Figure S589. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S590. Gene #61: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 32(17Q21.31) MUTATED	55	76	19	30	46
DEL PEAK 32(17Q21.31) WILD-TYPE	125	63	80	81	87

Figure S590. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.079

Table S591. Gene #61: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 32(17Q21.31) MUTATED	128	70	28
DEL PEAK 32(17Q21.31) WILD-TYPE	177	177	82

Figure S591. Get High-res Image Gene #61: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.023

Table S592. Gene #62: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 33(18Q23) MUTATED	6	13	38	38	18	37	6	9
DEL PEAK 33(18Q23) WILD-TYPE	15	23	81	58	91	35	14	31

Figure S592. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.01

Table S593. Gene #62: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 33(18Q23) MUTATED	31	35	54	35	10
DEL PEAK 33(18Q23) WILD-TYPE	70	117	60	53	48

Figure S593. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S594. Gene #62: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 33(18Q23) MUTATED	110	68	32	131	13
DEL PEAK 33(18Q23) WILD-TYPE	150	344	61	134	36

Figure S594. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S595. Gene #62: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 33(18Q23) MUTATED	59	47	88	17	30
DEL PEAK 33(18Q23) WILD-TYPE	73	150	89	71	98

Figure S595. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S596. Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 33(18Q23) MUTATED	171	133	47
DEL PEAK 33(18Q23) WILD-TYPE	372	165	185

Figure S596. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S597. Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 33(18Q23) MUTATED	52	95	81	19	77	27
DEL PEAK 33(18Q23) WILD-TYPE	167	69	225	122	106	33

Figure S597. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S598. Gene #62: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 33(18Q23) MUTATED	144	63	143
DEL PEAK 33(18Q23) WILD-TYPE	187	190	333

Figure S598. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S599. Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 33(18Q23) MUTATED	89	76	81	32	18	54
DEL PEAK 33(18Q23) WILD-TYPE	142	84	241	95	68	80

Figure S599. Get High-res Image Gene #62: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S600. Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 34(19P13.3) MUTATED	7	10	48	57	13	35	6	6
DEL PEAK 34(19P13.3) WILD-TYPE	14	26	71	39	96	37	14	34

Figure S600. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S601. Gene #63: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 34(19P13.3) MUTATED	44	28	54	53	3
DEL PEAK 34(19P13.3) WILD-TYPE	57	124	60	35	55

Figure S601. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S602. Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 34(19P13.3) MUTATED	133	37	14	162	17
DEL PEAK 34(19P13.3) WILD-TYPE	127	375	79	103	32

Figure S602. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S603. Gene #63: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 34(19P13.3) MUTATED	74	34	68	12	34
DEL PEAK 34(19P13.3) WILD-TYPE	58	163	109	76	94

Figure S603. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S604. Gene #63: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 34(19P13.3) MUTATED	81	36	32
DEL PEAK 34(19P13.3) WILD-TYPE	68	96	85

Figure S604. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S605. Gene #63: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 34(19P13.3) MUTATED	6	31	50	45	17
DEL PEAK 34(19P13.3) WILD-TYPE	58	75	40	62	14

Figure S605. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S606. Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 34(19P13.3) MUTATED	175	157	29
DEL PEAK 34(19P13.3) WILD-TYPE	368	141	203

Figure S606. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S607. Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 34(19P13.3) MUTATED	77	88	58	10	108	20
DEL PEAK 34(19P13.3) WILD-TYPE	142	76	248	131	75	40

Figure S607. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S608. Gene #63: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 34(19P13.3) MUTATED	187	47	119
DEL PEAK 34(19P13.3) WILD-TYPE	144	206	357

Figure S608. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S609. Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 34(19P13.3) MUTATED	96	74	49	26	23	85
DEL PEAK 34(19P13.3) WILD-TYPE	135	86	273	101	63	49

Figure S609. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S610. Gene #63: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 34(19P13.3) MUTATED	62	82	17	18	37
DEL PEAK 34(19P13.3) WILD-TYPE	118	57	82	93	96

Figure S610. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S611. Gene #63: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 34(19P13.3) MUTATED	139	60	17
DEL PEAK 34(19P13.3) WILD-TYPE	166	187	93

Figure S611. Get High-res Image Gene #63: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S612. Gene #64: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 35(19Q13.32) MUTATED	4	7	23	26	7	28	1	3
DEL PEAK 35(19Q13.32) WILD-TYPE	17	29	96	70	102	44	19	37

Figure S612. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S613. Gene #64: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 35(19Q13.32) MUTATED	26	11	36	24	2
DEL PEAK 35(19Q13.32) WILD-TYPE	75	141	78	64	56

Figure S613. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S614. Gene #64: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 35(19Q13.32) MUTATED	88	23	8	89	8
DEL PEAK 35(19Q13.32) WILD-TYPE	172	389	85	176	41

Figure S614. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S615. Gene #64: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 35(19Q13.32) MUTATED	47	19	47	8	18
DEL PEAK 35(19Q13.32) WILD-TYPE	85	178	130	80	110

Figure S615. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.11

Table S616. Gene #64: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 35(19Q13.32) MUTATED	45	20	15
DEL PEAK 35(19Q13.32) WILD-TYPE	104	112	102

Figure S616. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.008

Table S617. Gene #64: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 35(19Q13.32) MUTATED	4	12	30	23	11
DEL PEAK 35(19Q13.32) WILD-TYPE	60	94	60	84	20

Figure S617. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S618. Gene #64: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 35(19Q13.32) MUTATED	103	99	13
DEL PEAK 35(19Q13.32) WILD-TYPE	440	199	219

Figure S618. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S619. Gene #64: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 35(19Q13.32) MUTATED	50	56	25	8	58	18
DEL PEAK 35(19Q13.32) WILD-TYPE	169	108	281	133	125	42

Figure S619. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S620. Gene #64: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 35(19Q13.32) MUTATED	109	27	73
DEL PEAK 35(19Q13.32) WILD-TYPE	222	226	403

Figure S620. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S621. Gene #64: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 35(19Q13.32) MUTATED	62	44	21	20	16	46
DEL PEAK 35(19Q13.32) WILD-TYPE	169	116	301	107	70	88

Figure S621. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S622. Gene #64: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 35(19Q13.32) MUTATED	43	50	16	7	18
DEL PEAK 35(19Q13.32) WILD-TYPE	137	89	83	104	115

Figure S622. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S623. Gene #64: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 35(19Q13.32) MUTATED	92	36	6
DEL PEAK 35(19Q13.32) WILD-TYPE	213	211	104

Figure S623. Get High-res Image Gene #64: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S624. Gene #65: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 36(20P13) MUTATED	1	3	28	25	3	16	3	1
DEL PEAK 36(20P13) WILD-TYPE	20	33	91	71	106	56	17	39

Figure S624. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S625. Gene #65: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 36(20P13) MUTATED	23	9	25	23	0
DEL PEAK 36(20P13) WILD-TYPE	78	143	89	65	58

Figure S625. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S626. Gene #65: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 36(20P13) MUTATED	46	20	7	78	9
DEL PEAK 36(20P13) WILD-TYPE	214	392	86	187	40

Figure S626. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S627. Gene #65: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 36(20P13) MUTATED	44	11	29	8	10
DEL PEAK 36(20P13) WILD-TYPE	88	186	148	80	118

Figure S627. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.074

Table S628. Gene #65: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 36(20P13) MUTATED	37	10	17
DEL PEAK 36(20P13) WILD-TYPE	112	122	100

Figure S628. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.16

Table S629. Gene #65: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 36(20P13) MUTATED	5	8	24	20	7
DEL PEAK 36(20P13) WILD-TYPE	59	98	66	87	24

Figure S629. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S630. Gene #65: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 36(20P13) MUTATED	69	81	9
DEL PEAK 36(20P13) WILD-TYPE	474	217	223

Figure S630. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S631. Gene #65: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 36(20P13) MUTATED	35	33	21	3	56	11
DEL PEAK 36(20P13) WILD-TYPE	184	131	285	138	127	49

Figure S631. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S632. Gene #65: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	331	253	476
DEL PEAK 36(20P13) MUTATED	88	16	47
DEL PEAK 36(20P13) WILD-TYPE	243	237	429

Figure S632. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S633. Gene #65: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 36(20P13) MUTATED	36	36	16	7	13	43
DEL PEAK 36(20P13) WILD-TYPE	195	124	306	120	73	91

Figure S633. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S634. Gene #65: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	180	139	99	111	133
DEL PEAK 36(20P13) MUTATED	21	46	9	6	11
DEL PEAK 36(20P13) WILD-TYPE	159	93	90	105	122

Figure S634. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S635. Gene #65: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	305	247	110
DEL PEAK 36(20P13) MUTATED	72	20	1
DEL PEAK 36(20P13) WILD-TYPE	233	227	109

Figure S635. Get High-res Image Gene #65: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S636. Gene #66: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 37(21Q11.2) MUTATED	3	11	37	16	11	23	3	4
DEL PEAK 37(21Q11.2) WILD-TYPE	18	25	82	80	98	49	17	36

Figure S636. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S637. Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 37(21Q11.2) MUTATED	89	33	17	68	10
DEL PEAK 37(21Q11.2) WILD-TYPE	171	379	76	197	39

Figure S637. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.055

Table S638. Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 37(21Q11.2) MUTATED	22	38	53	8	18
DEL PEAK 37(21Q11.2) WILD-TYPE	110	159	124	80	110

Figure S638. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.061

Table S639. Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 37(21Q11.2) MUTATED	126	63	26
DEL PEAK 37(21Q11.2) WILD-TYPE	417	235	206

Figure S639. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S640. Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 37(21Q11.2) MUTATED	51	57	48	14	31	14
DEL PEAK 37(21Q11.2) WILD-TYPE	168	107	258	127	152	46

Figure S640. Get High-res Image Gene #66: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.008

Table S641. Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	260	412	93	265	49
DEL PEAK 38(22Q13.32) MUTATED	145	141	58	126	22
DEL PEAK 38(22Q13.32) WILD-TYPE	115	271	35	139	27

Figure S641. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.23

Table S642. Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	543	298	232
DEL PEAK 38(22Q13.32) MUTATED	277	123	89
DEL PEAK 38(22Q13.32) WILD-TYPE	266	175	143

Figure S642. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.12

Table S643. Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	219	164	306	141	183	60
DEL PEAK 38(22Q13.32) MUTATED	119	89	131	54	77	19
DEL PEAK 38(22Q13.32) WILD-TYPE	100	75	175	87	106	41

Figure S643. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.14

Table S644. Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	231	160	322	127	86	134
DEL PEAK 38(22Q13.32) MUTATED	117	76	122	75	37	56
DEL PEAK 38(22Q13.32) WILD-TYPE	114	84	200	52	49	78

Figure S644. Get High-res Image Gene #67: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 1079
Number of significantly focal cnvs = 67
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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