Correlation between copy number variation genes (focal events) and molecular subtypes

Stomach Adenocarcinoma (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1V98753

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 89 focal events and 10 molecular subtypes across 441 patients, 595 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q42.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_9p13.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_10q26.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_11p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_xq27.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1q44 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
del_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q33.3 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10p12.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_18q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 89 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 595 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1q21 3	160 (36%)	281	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0325 (0.0513)	0.0284 (0.046)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00013 (0.000371)
del 9p21 3	193 (44%)	248	1e-05 (3.82e-05)	1e-05 (3.82e-05)	5e-05 (0.000155)	2e-05 (7.01e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.028 (0.0455)	0.0313 (0.0498)
del 19p13 3	162 (37%)	279	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00422 (0.00824)	0.00448 (0.00857)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)
del 22q13 31	161 (37%)	280	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0497 (0.0743)	0.00602 (0.0112)	0.00134 (0.00296)	0.00426 (0.00824)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00016 (0.000448)	0.0143 (0.0244)
amp 17q12	147 (33%)	294	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.795 (0.817)	0.0396 (0.061)	0.00014 (0.000396)	0.00021 (0.000568)	1e-05 (3.82e-05)	3e-05 (9.85e-05)	0.00444 (0.00852)	0.00024 (0.000638)
amp 19q12	130 (29%)	311	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00639 (0.0118)	0.113 (0.152)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0486 (0.073)
amp 20q13 2	293 (66%)	148	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00642 (0.0118)	0.0118 (0.0205)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	3e-05 (9.85e-05)	0.0764 (0.107)
del 1p36 11	135 (31%)	306	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.158 (0.202)	0.00089 (0.00204)	0.00031 (0.000793)	3e-05 (9.85e-05)	2e-05 (7.01e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.00331 (0.00663)
del 3q26 31	47 (11%)	394	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.0347 (0.0542)	0.0475 (0.0717)	0.00052 (0.00126)	4e-05 (0.000126)	2e-05 (7.01e-05)	0.005 (0.00949)	0.00432 (0.00834)	0.076 (0.107)
del 9p23	195 (44%)	246	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0295 (0.0475)	0.00101 (0.00229)	2e-05 (7.01e-05)	0.00213 (0.00446)	4e-05 (0.000126)	0.00018 (0.000498)	0.149 (0.192)	0.00365 (0.00725)
del 10q23 31	116 (26%)	325	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.0632 (0.091)	0.00024 (0.000638)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.00199 (0.00422)	0.0487 (0.0731)
del 15q11 2	120 (27%)	321	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00184 (0.00396)	0.266 (0.317)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00038 (0.000955)	3e-05 (9.85e-05)	0.0287 (0.0463)	0.00033 (0.000842)
del 15q15 1	122 (28%)	319	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00383 (0.00754)	0.293 (0.343)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)	3e-05 (9.85e-05)	0.00611 (0.0113)	0.00019 (0.000522)
del 17p12	181 (41%)	260	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.401 (0.448)	0.00783 (0.0142)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0156 (0.0263)	0.00014 (0.000396)
amp 3q26 2	164 (37%)	277	1e-05 (3.82e-05)	0.00023 (0.000615)	0.856 (0.869)	0.00387 (0.0076)	0.399 (0.447)	0.0106 (0.0185)	0.0044 (0.00846)	0.0167 (0.028)	0.00329 (0.00661)	0.0143 (0.0244)
amp 5p15 33	130 (29%)	311	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.123 (0.164)	0.985 (0.987)	1e-05 (3.82e-05)	5e-05 (0.000155)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00031 (0.000793)	0.00058 (0.0014)
amp 5p13 1	126 (29%)	315	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.735 (0.765)	0.861 (0.873)	1e-05 (3.82e-05)	0.00059 (0.00142)	5e-05 (0.000155)	1e-05 (3.82e-05)	0.0159 (0.0268)	0.0302 (0.0485)
amp 6p21 1	124 (28%)	317	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.35 (0.4)	0.234 (0.283)	0.0002 (0.000546)	9e-05 (0.000268)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00012 (0.000343)	0.00039 (0.000975)
amp 6q12	88 (20%)	353	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0677 (0.0966)	0.88 (0.891)	8e-05 (0.000241)	0.00027 (0.000709)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0135 (0.0233)
amp 6q21	82 (19%)	359	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.386 (0.434)	0.404 (0.451)	0.00143 (0.00314)	0.00158 (0.00346)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00023 (0.000615)	0.00086 (0.00198)
amp 7p22 1	229 (52%)	212	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.639 (0.678)	0.833 (0.85)	0.00012 (0.000343)	1e-05 (3.82e-05)	0.00469 (0.00896)	9e-05 (0.000268)	0.0441 (0.067)	0.0018 (0.00388)
amp 8q24 21	309 (70%)	132	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.383 (0.432)	0.381 (0.431)	0.00532 (0.00999)	0.0103 (0.0181)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0006 (0.00144)	0.00496 (0.00943)
amp 10p11 22	119 (27%)	322	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.147 (0.191)	0.522 (0.565)	0.00122 (0.00275)	0.00929 (0.0164)	0.00131 (0.00291)	7e-05 (0.000213)	0.00304 (0.00615)	0.0181 (0.03)
amp 11p11 2	92 (21%)	349	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.697 (0.734)	0.169 (0.216)	3e-05 (9.85e-05)	0.00036 (0.000908)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00036 (0.000908)	0.00317 (0.00638)
amp 13q22 1	181 (41%)	260	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.256 (0.307)	0.724 (0.756)	3e-05 (9.85e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	4e-05 (0.000126)	0.0345 (0.0541)
amp 15q26 1	113 (26%)	328	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.149 (0.193)	0.24 (0.289)	7e-05 (0.000213)	3e-05 (9.85e-05)	0.0005 (0.00122)	0.00028 (0.000729)	0.00775 (0.0141)	0.00086 (0.00198)
del 3p26 1	143 (32%)	298	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.343 (0.393)	0.193 (0.241)	0.00619 (0.0115)	5e-05 (0.000155)	2e-05 (7.01e-05)	1e-05 (3.82e-05)	0.00011 (0.000321)	0.0055 (0.0103)
del 3p14 2	158 (36%)	283	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.41 (0.455)	0.373 (0.423)	0.0001 (0.000295)	0.00028 (0.000729)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00424 (0.00824)	0.00022 (0.000592)
del 4p16 3	169 (38%)	272	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.456 (0.503)	0.201 (0.25)	1e-05 (3.82e-05)	3e-05 (9.85e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00031 (0.000793)	0.0119 (0.0205)
del 4q34 3	200 (45%)	241	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.052 (0.0775)	0.00872 (0.0156)	2e-05 (7.01e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0129 (0.0223)	0.0856 (0.119)
del 5q12 1	170 (39%)	271	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.232 (0.281)	0.177 (0.223)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)
del 5q23 2	158 (36%)	283	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.136 (0.179)	0.0747 (0.106)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)
del 6q26	102 (23%)	339	1e-05 (3.82e-05)	0.0344 (0.0541)	0.792 (0.816)	0.699 (0.735)	0.00082 (0.00192)	0.00215 (0.00449)	0.0411 (0.0629)	0.00731 (0.0133)	0.00299 (0.00606)	0.00213 (0.00446)
del 7q36 3	98 (22%)	343	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.384 (0.432)	0.0766 (0.108)	2e-05 (7.01e-05)	0.0004 (0.000997)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00338 (0.00676)	0.00816 (0.0147)
del 8p23 3	126 (29%)	315	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0749 (0.106)	0.592 (0.634)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)	3e-05 (9.85e-05)	0.00895 (0.0159)	8e-05 (0.000241)
del 11p15 5	97 (22%)	344	1e-05 (3.82e-05)	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.00516 (0.00973)	0.0037 (0.00733)	0.0307 (0.0491)	7e-05 (0.000213)	0.00141 (0.00311)	0.207 (0.255)	0.535 (0.578)
del 14q23 3	136 (31%)	305	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.754 (0.782)	0.427 (0.473)	2e-05 (7.01e-05)	0.00027 (0.000709)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0463 (0.0702)	0.00269 (0.00554)
del 16q23 1	182 (41%)	259	1e-05 (3.82e-05)	0.00039 (0.000975)	0.468 (0.513)	0.17 (0.216)	0.00171 (0.00371)	0.00882 (0.0158)	0.00012 (0.000343)	0.00379 (0.00748)	0.00912 (0.0161)	0.0331 (0.0522)
del 17p13 3	176 (40%)	265	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.552 (0.595)	0.0201 (0.033)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	7e-05 (0.000213)	0.0631 (0.091)	0.00272 (0.00559)
del 18q21 2	204 (46%)	237	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.668 (0.706)	0.45 (0.496)	0.0003 (0.000774)	0.00423 (0.00824)	4e-05 (0.000126)	0.00193 (0.0041)	0.00133 (0.00294)	0.00942 (0.0166)
del 19q13 11	75 (17%)	366	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0647 (0.093)	0.712 (0.746)	2e-05 (7.01e-05)	0.00068 (0.00162)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00572 (0.0107)	0.00895 (0.0159)
amp 1q42 3	150 (34%)	291	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.405 (0.452)	0.097 (0.133)	1e-05 (3.82e-05)	0.00012 (0.000343)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.16 (0.205)
amp 7p11 2	214 (49%)	227	1e-05 (3.82e-05)	3e-05 (9.85e-05)	0.904 (0.912)	0.853 (0.867)	0.0419 (0.064)	0.00043 (0.00107)	0.0323 (0.0512)	0.00259 (0.00535)	0.0959 (0.131)	0.00308 (0.00622)
amp 11p13	88 (20%)	353	1e-05 (3.82e-05)	0.00028 (0.000729)	0.645 (0.684)	0.116 (0.155)	0.00074 (0.00173)	0.00521 (0.0098)	3e-05 (9.85e-05)	0.00017 (0.000473)	0.033 (0.0521)	0.502 (0.545)
amp 11q13 3	115 (26%)	326	1e-05 (3.82e-05)	0.00376 (0.00744)	0.188 (0.236)	0.637 (0.678)	0.128 (0.17)	0.0379 (0.0587)	2e-05 (7.01e-05)	0.00298 (0.00606)	0.0013 (0.00289)	0.0477 (0.0718)
amp 13q12 3	170 (39%)	271	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.327 (0.378)	0.151 (0.194)	0.0171 (0.0284)	4e-05 (0.000126)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.00019 (0.000522)	0.0612 (0.0888)
amp 19q13 32	111 (25%)	330	1e-05 (3.82e-05)	0.0106 (0.0185)	0.385 (0.433)	0.476 (0.521)	0.00123 (0.00276)	0.0845 (0.118)	0.00086 (0.00198)	0.00475 (0.00905)	0.00245 (0.00508)	0.00872 (0.0156)
del 1p13 2	94 (21%)	347	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0805 (0.113)	0.0659 (0.0945)	0.00099 (0.00225)	0.00084 (0.00195)	0.00189 (0.00403)	0.00725 (0.0132)	0.139 (0.182)	0.0161 (0.0271)
del 6p25 3	115 (26%)	326	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.138 (0.182)	0.822 (0.839)	0.0001 (0.000295)	6e-05 (0.000185)	3e-05 (9.85e-05)	1e-05 (3.82e-05)	0.11 (0.149)	0.0466 (0.0706)
del 9q21 11	114 (26%)	327	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.137 (0.181)	0.0565 (0.0831)	0.00156 (0.00342)	0.0361 (0.0561)	3e-05 (9.85e-05)	1e-05 (3.82e-05)	0.0365 (0.0566)	0.102 (0.139)
del 10q22 3	79 (18%)	362	1e-05 (3.82e-05)	0.00018 (0.000498)	0.846 (0.861)	0.0894 (0.123)	0.00026 (0.000687)	0.00057 (0.00137)	4e-05 (0.000126)	4e-05 (0.000126)	0.0278 (0.0452)	0.0574 (0.0838)
del 12p13 1	77 (17%)	364	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.54 (0.584)	0.421 (0.466)	1e-05 (3.82e-05)	3e-05 (9.85e-05)	0.00036 (0.000908)	0.00355 (0.00707)	0.204 (0.253)	0.0496 (0.0743)
del 16p13 3	93 (21%)	348	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.702 (0.737)	0.816 (0.835)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.0891 (0.123)
del 18q12 2	181 (41%)	260	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.913 (0.919)	0.738 (0.767)	0.00425 (0.00824)	0.0587 (0.0853)	9e-05 (0.000268)	0.00036 (0.000908)	0.00088 (0.00202)	0.00724 (0.0132)
del 21q11 2	183 (41%)	258	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.236 (0.285)	0.146 (0.19)	0.00286 (0.00584)	0.00209 (0.0044)	3e-05 (9.85e-05)	0.00073 (0.00171)	0.0016 (0.00349)	0.0923 (0.127)
del 21q22 3	193 (44%)	248	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.199 (0.248)	0.293 (0.343)	0.0055 (0.0103)	0.0005 (0.00122)	0.00021 (0.000568)	0.00294 (0.00599)	0.00026 (0.000687)	0.0933 (0.128)
amp 1p36 22	66 (15%)	375	1e-05 (3.82e-05)	5e-05 (0.000155)	0.515 (0.559)	0.245 (0.294)	0.00014 (0.000396)	0.121 (0.161)	0.011 (0.0191)	0.00072 (0.0017)	0.133 (0.177)	0.00884 (0.0158)
amp 7q21 2	204 (46%)	237	1e-05 (3.82e-05)	8e-05 (0.000241)	0.216 (0.265)	0.77 (0.795)	0.461 (0.507)	4e-05 (0.000126)	0.0285 (0.0461)	0.00205 (0.00433)	0.0996 (0.136)	0.0087 (0.0156)
amp 18q11 2	140 (32%)	301	1e-05 (3.82e-05)	4e-05 (0.000126)	0.291 (0.341)	0.286 (0.336)	0.0151 (0.0257)	0.00397 (0.00778)	0.00046 (0.00113)	0.00128 (0.00286)	0.362 (0.413)	0.317 (0.369)
del 2q37 2	72 (16%)	369	1e-05 (3.82e-05)	2e-05 (7.01e-05)	0.327 (0.378)	0.239 (0.289)	0.00275 (0.00564)	0.175 (0.222)	0.0013 (0.00289)	1e-05 (3.82e-05)	0.218 (0.267)	0.0164 (0.0274)
del 4q22 1	193 (44%)	248	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.108 (0.146)	0.268 (0.318)	0.00241 (0.00502)	4e-05 (0.000126)	0.00084 (0.00195)	0.00055 (0.00133)	0.583 (0.627)	0.12 (0.161)
del 6q24 3	78 (18%)	363	1e-05 (3.82e-05)	0.00186 (0.00398)	0.814 (0.835)	1 (1.00)	0.0137 (0.0236)	0.0225 (0.0368)	0.246 (0.295)	0.0303 (0.0486)	0.0141 (0.0242)	0.0579 (0.0843)
del 14q32 32	133 (30%)	308	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.766 (0.792)	0.589 (0.631)	0.00174 (0.00377)	0.0005 (0.00122)	0.00011 (0.000321)	0.00703 (0.0129)	0.257 (0.307)	0.0567 (0.0832)
del 17q24 3	76 (17%)	365	1e-05 (3.82e-05)	0.00016 (0.000448)	0.18 (0.227)	0.265 (0.316)	0.0182 (0.03)	0.0051 (0.00966)	0.00644 (0.0118)	0.0411 (0.0629)	0.233 (0.283)	0.561 (0.603)
del xp22 2	85 (19%)	356	1e-05 (3.82e-05)	0.00021 (0.000568)	0.466 (0.512)	0.0428 (0.0652)	0.00012 (0.000343)	0.0003 (0.000774)	0.0517 (0.077)	0.00284 (0.00581)	0.337 (0.388)	0.283 (0.334)
amp 7q22 1	202 (46%)	239	1e-05 (3.82e-05)	0.00071 (0.00168)	0.227 (0.276)	0.886 (0.896)	0.768 (0.793)	0.00176 (0.0038)	0.1 (0.136)	0.0299 (0.0481)	0.147 (0.191)	0.0165 (0.0277)
amp 10q22 2	88 (20%)	353	1e-05 (3.82e-05)	0.039 (0.0601)	0.0196 (0.0322)	0.205 (0.253)	0.0153 (0.0259)	0.0229 (0.0373)	0.253 (0.303)	0.139 (0.182)	0.278 (0.329)	0.289 (0.339)
amp 10q26 13	88 (20%)	353	1e-05 (3.82e-05)	0.00015 (0.000422)	0.0361 (0.0561)	0.327 (0.378)	0.00637 (0.0118)	0.0316 (0.0502)	0.203 (0.252)	0.201 (0.25)	0.822 (0.839)	0.587 (0.631)
del 1q44	30 (7%)	411	0.00052 (0.00126)	0.00193 (0.0041)	0.178 (0.225)	0.111 (0.15)	0.362 (0.413)	0.027 (0.044)	0.00514 (0.00971)	0.147 (0.191)	0.897 (0.907)	0.0172 (0.0285)
del 6q14 1	89 (20%)	352	1e-05 (3.82e-05)	0.0002 (0.000546)	0.213 (0.262)	0.843 (0.858)	0.00045 (0.00111)	0.00439 (0.00846)	0.102 (0.139)	0.00089 (0.00204)	0.107 (0.144)	0.193 (0.242)
del 11q23 2	99 (22%)	342	1e-05 (3.82e-05)	0.00098 (0.00224)	0.703 (0.737)	0.152 (0.196)	0.00099 (0.00225)	0.00011 (0.000321)	0.196 (0.245)	0.0725 (0.103)	0.0293 (0.0472)	0.189 (0.237)
del 20p12 1	39 (9%)	402	0.00111 (0.00251)	0.00022 (0.000592)	0.658 (0.696)	0.189 (0.237)	0.0156 (0.0263)	0.0839 (0.117)	0.00126 (0.00282)	0.055 (0.0811)	0.662 (0.7)	0.04 (0.0615)
del xq21 33	56 (13%)	385	1e-05 (3.82e-05)	0.0042 (0.00822)	0.816 (0.835)	0.035 (0.0547)	0.00806 (0.0146)	0.0513 (0.0765)	0.0132 (0.0229)	0.0616 (0.0891)	0.0957 (0.131)	0.0588 (0.0853)
amp 9q34 3	122 (28%)	319	3e-05 (9.85e-05)	0.0142 (0.0244)	0.722 (0.754)	0.472 (0.517)	0.0452 (0.0686)	0.139 (0.182)	0.0106 (0.0185)	0.332 (0.382)	0.157 (0.202)	0.273 (0.324)
amp 12p12 1	128 (29%)	313	1e-05 (3.82e-05)	0.0311 (0.0495)	0.43 (0.475)	0.35 (0.4)	0.207 (0.255)	0.365 (0.415)	0.0365 (0.0566)	0.137 (0.181)	0.608 (0.648)	0.0418 (0.0639)
amp xq27 3	86 (20%)	355	1e-05 (3.82e-05)	0.009 (0.016)	0.37 (0.421)	0.943 (0.946)	0.468 (0.513)	0.00012 (0.000343)	0.0537 (0.0795)	0.389 (0.437)	0.0527 (0.0784)	0.0153 (0.0259)
del 2q32 1	64 (15%)	377	0.0003 (0.000774)	0.00044 (0.00109)	0.488 (0.531)	0.0828 (0.116)	0.0909 (0.125)	0.239 (0.289)	0.0169 (0.0282)	0.00073 (0.00171)	0.217 (0.265)	0.0889 (0.123)
del 7q31 1	71 (16%)	370	1e-05 (3.82e-05)	0.00063 (0.0015)	0.713 (0.746)	0.499 (0.542)	0.00919 (0.0162)	0.279 (0.33)	0.00071 (0.00168)	0.0698 (0.0995)	0.0649 (0.0932)	0.127 (0.17)
del 10p12 31	67 (15%)	374	1e-05 (3.82e-05)	0.00186 (0.00398)	0.207 (0.255)	0.413 (0.458)	0.171 (0.218)	0.499 (0.542)	4e-05 (0.000126)	0.00161 (0.0035)	0.293 (0.343)	0.206 (0.255)
del xp21 1	74 (17%)	367	1e-05 (3.82e-05)	0.00339 (0.00676)	0.163 (0.208)	0.0313 (0.0498)	0.00861 (0.0155)	0.0622 (0.0899)	0.131 (0.174)	0.243 (0.292)	0.484 (0.528)	0.617 (0.656)
amp 8p23 1	177 (40%)	264	1e-05 (3.82e-05)	0.0001 (0.000295)	0.589 (0.631)	0.602 (0.643)	0.0548 (0.0809)	0.0176 (0.0291)	0.139 (0.182)	0.0668 (0.0956)	0.12 (0.161)	0.0536 (0.0795)
amp 9p24 1	65 (15%)	376	4e-05 (0.000126)	0.0846 (0.118)	0.616 (0.656)	0.221 (0.27)	0.108 (0.146)	0.00533 (0.00999)	0.0332 (0.0523)	0.327 (0.378)	0.0568 (0.0832)	0.14 (0.183)
amp 9p13 2	91 (21%)	350	0.00043 (0.00107)	0.285 (0.336)	0.383 (0.432)	0.327 (0.378)	0.0146 (0.0248)	0.266 (0.317)	0.057 (0.0834)	0.298 (0.347)	0.00209 (0.0044)	0.184 (0.232)
del 12q12	59 (13%)	382	1e-05 (3.82e-05)	1e-05 (3.82e-05)	0.921 (0.927)	0.931 (0.935)	0.0974 (0.133)	0.143 (0.186)	0.305 (0.355)	0.0383 (0.0592)	0.794 (0.817)	0.69 (0.727)
del 13q12 11	63 (14%)	378	1e-05 (3.82e-05)	0.0475 (0.0717)	0.423 (0.469)	0.364 (0.415)	0.0677 (0.0966)	0.0218 (0.0357)	0.0748 (0.106)	0.276 (0.326)	0.988 (0.989)	0.372 (0.422)
amp 12q15	109 (25%)	332	1e-05 (3.82e-05)	0.0197 (0.0323)	0.22 (0.268)	0.33 (0.38)	0.276 (0.326)	0.0752 (0.106)	0.134 (0.178)	0.169 (0.215)	0.0542 (0.0801)	0.216 (0.265)
del 1q44	26 (6%)	415	0.0025 (0.00517)	0.00245 (0.00508)	0.309 (0.359)	0.376 (0.425)	0.739 (0.767)	0.341 (0.391)	0.219 (0.268)	0.749 (0.777)	0.408 (0.454)	0.551 (0.595)
del 2q33 3	49 (11%)	392	0.00017 (0.000473)	0.0715 (0.102)	0.4 (0.447)	0.645 (0.684)	0.175 (0.222)	0.807 (0.829)	0.0875 (0.122)	0.00956 (0.0168)	0.154 (0.199)	0.0894 (0.123)
amp 19p13 2	47 (11%)	394	1e-05 (3.82e-05)	0.0571 (0.0834)	0.905 (0.912)	0.758 (0.784)	0.734 (0.765)	0.162 (0.208)	0.479 (0.523)	0.701 (0.736)	0.104 (0.141)	0.409 (0.455)

'amp_1p36.22' versus 'CN_CNMF'

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

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

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

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

'amp_1p36.22' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_1p36.22' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 1(1P36.22) MUTATED	2	2	6	6	16
AMP PEAK 1(1P36.22) WILD-TYPE	63	60	40	31	46

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

'amp_1p36.22' versus 'MIRSEQ_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.019

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 1(1P36.22) MUTATED	28	11	26
AMP PEAK 1(1P36.22) WILD-TYPE	158	122	95

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

'amp_1p36.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0017

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 1(1P36.22) MUTATED	15	20	4	26
AMP PEAK 1(1P36.22) WILD-TYPE	64	155	75	81

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

'amp_1p36.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00884 (Fisher's exact test), Q value = 0.016

Table S6. Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 1(1P36.22) MUTATED	32	3	14
AMP PEAK 1(1P36.22) WILD-TYPE	169	70	58

Figure S6. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

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

Table S7. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S7. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.051

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
AMP PEAK 2(1Q21.3) MUTATED	34	23	38
AMP PEAK 2(1Q21.3) WILD-TYPE	48	67	53

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

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.046

Table S10. Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
AMP PEAK 2(1Q21.3) MUTATED	11	40	20	24
AMP PEAK 2(1Q21.3) WILD-TYPE	23	43	35	67

Figure S10. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

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

Table S11. Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 2(1Q21.3) MUTATED	12	10	16	13	47
AMP PEAK 2(1Q21.3) WILD-TYPE	53	52	30	24	15

Figure S11. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S12. Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 2(1Q21.3) MUTATED	12	3	7	26	22	27	1
AMP PEAK 2(1Q21.3) WILD-TYPE	26	18	42	36	19	13	20

Figure S12. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

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

Table S13. Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 2(1Q21.3) MUTATED	56	30	73
AMP PEAK 2(1Q21.3) WILD-TYPE	130	103	48

Figure S13. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S14. Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 2(1Q21.3) MUTATED	34	41	20	64
AMP PEAK 2(1Q21.3) WILD-TYPE	45	134	59	43

Figure S14. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S15. Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 2(1Q21.3) MUTATED	46	18	15	17	14	10
AMP PEAK 2(1Q21.3) WILD-TYPE	30	40	45	41	22	48

Figure S15. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00037

Table S16. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 2(1Q21.3) MUTATED	78	11	31
AMP PEAK 2(1Q21.3) WILD-TYPE	123	62	41

Figure S16. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

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

Table S17. Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S17. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

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

Table S18. Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S18. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

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

Table S19. Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 3(1Q42.3) MUTATED	13	13	12	12	41
AMP PEAK 3(1Q42.3) WILD-TYPE	52	49	34	25	21

Figure S19. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S20. Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 3(1Q42.3) MUTATED	12	3	10	20	20	24	2
AMP PEAK 3(1Q42.3) WILD-TYPE	26	18	39	42	21	16	19

Figure S20. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

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

Table S21. Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 3(1Q42.3) MUTATED	40	37	73
AMP PEAK 3(1Q42.3) WILD-TYPE	146	96	48

Figure S21. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S22. Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 3(1Q42.3) MUTATED	30	32	24	64
AMP PEAK 3(1Q42.3) WILD-TYPE	49	143	55	43

Figure S22. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S23. Gene #3: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 3(1Q42.3) MUTATED	43	12	16	17	16	11
AMP PEAK 3(1Q42.3) WILD-TYPE	33	46	44	41	20	47

Figure S23. Get High-res Image Gene #3: 'amp_1q42.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'CN_CNMF'

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

Table S24. Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S24. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00061

Table S25. Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S25. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00387 (Fisher's exact test), Q value = 0.0076

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
AMP PEAK 4(3Q26.2) MUTATED	15	26	9	39
AMP PEAK 4(3Q26.2) WILD-TYPE	19	57	46	52

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

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.018

Table S27. Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 4(3Q26.2) MUTATED	13	11	10	30	10	13	4
AMP PEAK 4(3Q26.2) WILD-TYPE	25	10	39	32	31	27	17

Figure S27. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 0.0044 (Fisher's exact test), Q value = 0.0085

Table S28. Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 4(3Q26.2) MUTATED	63	41	60
AMP PEAK 4(3Q26.2) WILD-TYPE	123	92	61

Figure S28. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.028

Table S29. Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 4(3Q26.2) MUTATED	27	62	22	53
AMP PEAK 4(3Q26.2) WILD-TYPE	52	113	57	54

Figure S29. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.0066

Table S30. Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 4(3Q26.2) MUTATED	40	23	20	18	13	11
AMP PEAK 4(3Q26.2) WILD-TYPE	36	35	40	40	23	47

Figure S30. Get High-res Image Gene #4: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.024

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 4(3Q26.2) MUTATED	81	16	28
AMP PEAK 4(3Q26.2) WILD-TYPE	120	57	44

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

'amp_5p15.33' versus 'CN_CNMF'

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

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

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

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

'amp_5p15.33' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_5p15.33' versus 'MRNASEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 5(5P15.33) MUTATED	11	6	10	10	38
AMP PEAK 5(5P15.33) WILD-TYPE	54	56	36	27	24

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

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S35. Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 5(5P15.33) MUTATED	7	5	6	16	16	23	2
AMP PEAK 5(5P15.33) WILD-TYPE	31	16	43	46	25	17	19

Figure S35. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

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

Table S36. Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 5(5P15.33) MUTATED	49	22	58
AMP PEAK 5(5P15.33) WILD-TYPE	137	111	63

Figure S36. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S37. Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 5(5P15.33) MUTATED	17	41	15	56
AMP PEAK 5(5P15.33) WILD-TYPE	62	134	64	51

Figure S37. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00079

Table S38. Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 5(5P15.33) MUTATED	35	13	19	18	12	6
AMP PEAK 5(5P15.33) WILD-TYPE	41	45	41	40	24	52

Figure S38. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.0014

Table S39. Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 5(5P15.33) MUTATED	70	9	24
AMP PEAK 5(5P15.33) WILD-TYPE	131	64	48

Figure S39. Get High-res Image Gene #5: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

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

Table S40. Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S40. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

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

Table S41. Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S41. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CNMF'

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

Table S42. Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 6(5P13.1) MUTATED	11	8	10	9	37
AMP PEAK 6(5P13.1) WILD-TYPE	54	54	36	28	25

Figure S42. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 6(5P13.1) MUTATED	9	4	7	17	14	22	2
AMP PEAK 6(5P13.1) WILD-TYPE	29	17	42	45	27	18	19

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

'amp_5p13.1' versus 'MIRSEQ_CNMF'

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

Table S44. Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 6(5P13.1) MUTATED	44	28	54
AMP PEAK 6(5P13.1) WILD-TYPE	142	105	67

Figure S44. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S45. Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 6(5P13.1) MUTATED	16	37	18	55
AMP PEAK 6(5P13.1) WILD-TYPE	63	138	61	52

Figure S45. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.027

Table S46. Gene #6: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 6(5P13.1) MUTATED	31	12	16	19	13	9
AMP PEAK 6(5P13.1) WILD-TYPE	45	46	44	39	23	49

Figure S46. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.049

Table S47. Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 6(5P13.1) MUTATED	68	13	19
AMP PEAK 6(5P13.1) WILD-TYPE	133	60	53

Figure S47. Get High-res Image Gene #6: 'amp_5p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p21.1' versus 'CN_CNMF'

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

Table S48. Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S48. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

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

Table S49. Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S49. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00055

Table S50. Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 7(6P21.1) MUTATED	10	10	10	11	30
AMP PEAK 7(6P21.1) WILD-TYPE	55	52	36	26	32

Figure S50. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S51. Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 7(6P21.1) MUTATED	10	1	5	17	15	20	3
AMP PEAK 7(6P21.1) WILD-TYPE	28	20	44	45	26	20	18

Figure S51. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 7(6P21.1) MUTATED	46	19	58
AMP PEAK 7(6P21.1) WILD-TYPE	140	114	63

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

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S53. Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 7(6P21.1) MUTATED	29	29	13	52
AMP PEAK 7(6P21.1) WILD-TYPE	50	146	66	55

Figure S53. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S54. Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 7(6P21.1) MUTATED	38	11	13	17	12	8
AMP PEAK 7(6P21.1) WILD-TYPE	38	47	47	41	24	50

Figure S54. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.00097

Table S55. Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 7(6P21.1) MUTATED	67	8	24
AMP PEAK 7(6P21.1) WILD-TYPE	134	65	48

Figure S55. Get High-res Image Gene #7: 'amp_6p21.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

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

Table S56. Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S56. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

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

Table S57. Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S57. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S58. Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 8(6Q12) MUTATED	6	7	9	6	26
AMP PEAK 8(6Q12) WILD-TYPE	59	55	37	31	36

Figure S58. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00071

Table S59. Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 8(6Q12) MUTATED	7	1	3	12	12	17	2
AMP PEAK 8(6Q12) WILD-TYPE	31	20	46	50	29	23	19

Figure S59. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

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

Table S60. Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 8(6Q12) MUTATED	30	15	42
AMP PEAK 8(6Q12) WILD-TYPE	156	118	79

Figure S60. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 8(6Q12) MUTATED	22	17	10	38
AMP PEAK 8(6Q12) WILD-TYPE	57	158	69	69

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

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S62. Gene #8: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 8(6Q12) MUTATED	32	6	6	9	8	5
AMP PEAK 8(6Q12) WILD-TYPE	44	52	54	49	28	53

Figure S62. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.023

Table S63. Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 8(6Q12) MUTATED	47	6	13
AMP PEAK 8(6Q12) WILD-TYPE	154	67	59

Figure S63. Get High-res Image Gene #8: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

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

Table S64. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S64. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

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

Table S65. Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S65. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0031

Table S66. Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 9(6Q21) MUTATED	7	7	8	5	23
AMP PEAK 9(6Q21) WILD-TYPE	58	55	38	32	39

Figure S66. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00158 (Fisher's exact test), Q value = 0.0035

Table S67. Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 9(6Q21) MUTATED	8	1	4	10	10	16	1
AMP PEAK 9(6Q21) WILD-TYPE	30	20	45	52	31	24	20

Figure S67. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

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

Table S68. Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 9(6Q21) MUTATED	29	11	41
AMP PEAK 9(6Q21) WILD-TYPE	157	122	80

Figure S68. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S69. Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 9(6Q21) MUTATED	16	19	7	39
AMP PEAK 9(6Q21) WILD-TYPE	63	156	72	68

Figure S69. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00061

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 9(6Q21) MUTATED	27	7	6	7	9	5
AMP PEAK 9(6Q21) WILD-TYPE	49	51	54	51	27	53

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

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.002

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 9(6Q21) MUTATED	44	3	14
AMP PEAK 9(6Q21) WILD-TYPE	157	70	58

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

'amp_7p22.1' versus 'CN_CNMF'

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

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

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

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

'amp_7p22.1' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_7p22.1' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 10(7P22.1) MUTATED	29	25	16	20	46
AMP PEAK 10(7P22.1) WILD-TYPE	36	37	30	17	16

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

'amp_7p22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 10(7P22.1) MUTATED	16	11	15	31	30	29	4
AMP PEAK 10(7P22.1) WILD-TYPE	22	10	34	31	11	11	17

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

'amp_7p22.1' versus 'MIRSEQ_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.009

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 10(7P22.1) MUTATED	98	55	75
AMP PEAK 10(7P22.1) WILD-TYPE	88	78	46

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

'amp_7p22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 10(7P22.1) MUTATED	46	79	30	73
AMP PEAK 10(7P22.1) WILD-TYPE	33	96	49	34

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

'amp_7p22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.067

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 10(7P22.1) MUTATED	47	28	29	29	23	21
AMP PEAK 10(7P22.1) WILD-TYPE	29	30	31	29	13	37

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

'amp_7p22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0039

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 10(7P22.1) MUTATED	112	24	41
AMP PEAK 10(7P22.1) WILD-TYPE	89	49	31

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

'amp_7p11.2' versus 'CN_CNMF'

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

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

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

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

'amp_7p11.2' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.064

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 11(7P11.2) MUTATED	28	24	15	19	37
AMP PEAK 11(7P11.2) WILD-TYPE	37	38	31	18	25

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

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.0011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 11(7P11.2) MUTATED	15	11	15	29	28	22	3
AMP PEAK 11(7P11.2) WILD-TYPE	23	10	34	33	13	18	18

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

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 0.051

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 11(7P11.2) MUTATED	92	53	68
AMP PEAK 11(7P11.2) WILD-TYPE	94	80	53

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

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00259 (Fisher's exact test), Q value = 0.0053

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 11(7P11.2) MUTATED	41	78	28	66
AMP PEAK 11(7P11.2) WILD-TYPE	38	97	51	41

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

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00308 (Fisher's exact test), Q value = 0.0062

Table S86. Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 11(7P11.2) MUTATED	102	22	40
AMP PEAK 11(7P11.2) WILD-TYPE	99	51	32

Figure S86. Get High-res Image Gene #11: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

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

Table S87. Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S87. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

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

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

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

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S89. Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 12(7Q21.2) MUTATED	14	13	14	26	30	19	3
AMP PEAK 12(7Q21.2) WILD-TYPE	24	8	35	36	11	21	18

Figure S89. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.046

Table S90. Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 12(7Q21.2) MUTATED	91	49	63
AMP PEAK 12(7Q21.2) WILD-TYPE	95	84	58

Figure S90. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00205 (Fisher's exact test), Q value = 0.0043

Table S91. Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 12(7Q21.2) MUTATED	46	71	27	59
AMP PEAK 12(7Q21.2) WILD-TYPE	33	104	52	48

Figure S91. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.016

Table S92. Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 12(7Q21.2) MUTATED	99	21	34
AMP PEAK 12(7Q21.2) WILD-TYPE	102	52	38

Figure S92. Get High-res Image Gene #12: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q22.1' versus 'CN_CNMF'

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

Table S93. Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S93. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q22.1' versus 'METHLYATION_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0017

Table S94. Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S94. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0038

Table S95. Gene #13: 'amp_7q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 13(7Q22.1) MUTATED	12	13	16	26	27	19	4
AMP PEAK 13(7Q22.1) WILD-TYPE	26	8	33	36	14	21	17

Figure S95. Get High-res Image Gene #13: 'amp_7q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_7q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.048

Table S96. Gene #13: 'amp_7q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 13(7Q22.1) MUTATED	42	72	29	58
AMP PEAK 13(7Q22.1) WILD-TYPE	37	103	50	49

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

'amp_7q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.028

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 13(7Q22.1) MUTATED	97	22	36
AMP PEAK 13(7Q22.1) WILD-TYPE	104	51	36

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

'amp_8p23.1' versus 'CN_CNMF'

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

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

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

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

'amp_8p23.1' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 14(8P23.1) MUTATED	14	7	22	28	14	8	14
AMP PEAK 14(8P23.1) WILD-TYPE	24	14	27	34	27	32	7

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

'amp_8q24.21' versus 'CN_CNMF'

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

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

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

Figure S101. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00532 (Fisher's exact test), Q value = 0.01

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 15(8Q24.21) MUTATED	42	36	23	23	51
AMP PEAK 15(8Q24.21) WILD-TYPE	23	26	23	14	11

Figure S103. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.018

Table S104. Gene #15: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 15(8Q24.21) MUTATED	22	9	28	37	29	34	16
AMP PEAK 15(8Q24.21) WILD-TYPE	16	12	21	25	12	6	5

Figure S104. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

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

Table S105. Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 15(8Q24.21) MUTATED	130	75	103
AMP PEAK 15(8Q24.21) WILD-TYPE	56	58	18

Figure S105. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S106. Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 15(8Q24.21) MUTATED	64	106	47	91
AMP PEAK 15(8Q24.21) WILD-TYPE	15	69	32	16

Figure S106. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

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

Table S107. Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 15(8Q24.21) MUTATED	64	45	41	36	25	29
AMP PEAK 15(8Q24.21) WILD-TYPE	12	13	19	22	11	29

Figure S107. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00496 (Fisher's exact test), Q value = 0.0094

Table S108. Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 15(8Q24.21) MUTATED	147	39	54
AMP PEAK 15(8Q24.21) WILD-TYPE	54	34	18

Figure S108. Get High-res Image Gene #15: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'CN_CNMF'

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

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

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

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

'amp_9p24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00533 (Fisher's exact test), Q value = 0.01

Table S110. Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 16(9P24.1) MUTATED	7	7	1	10	5	11	3
AMP PEAK 16(9P24.1) WILD-TYPE	31	14	48	52	36	29	18

Figure S110. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.052

Table S111. Gene #16: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 16(9P24.1) MUTATED	26	13	26
AMP PEAK 16(9P24.1) WILD-TYPE	160	120	95

Figure S111. Get High-res Image Gene #16: 'amp_9p24.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_9p13.2' versus 'CN_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0011

Table S112. Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S112. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.2' versus 'MRNASEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.025

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 17(9P13.2) MUTATED	11	3	11	9	14
AMP PEAK 17(9P13.2) WILD-TYPE	54	59	35	28	48

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

'amp_9p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0044

Table S114. Gene #17: 'amp_9p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 17(9P13.2) MUTATED	28	13	9	13	5	5
AMP PEAK 17(9P13.2) WILD-TYPE	48	45	51	45	31	53

Figure S114. Get High-res Image Gene #17: 'amp_9p13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_9q34.3' versus 'CN_CNMF'

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

Table S115. Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S115. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.024

Table S116. Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S116. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.069

Table S117. Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 18(9Q34.3) MUTATED	14	7	11	10	21
AMP PEAK 18(9Q34.3) WILD-TYPE	51	55	35	27	41

Figure S117. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.019

Table S118. Gene #18: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 18(9Q34.3) MUTATED	50	27	45
AMP PEAK 18(9Q34.3) WILD-TYPE	136	106	76

Figure S118. Get High-res Image Gene #18: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

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

Table S119. Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S119. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

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

Table S120. Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S120. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.0027

Table S121. Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 19(10P11.22) MUTATED	11	13	8	9	29
AMP PEAK 19(10P11.22) WILD-TYPE	54	49	38	28	33

Figure S121. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00929 (Fisher's exact test), Q value = 0.016

Table S122. Gene #19: 'amp_10p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 19(10P11.22) MUTATED	13	2	8	14	14	17	2
AMP PEAK 19(10P11.22) WILD-TYPE	25	19	41	48	27	23	19

Figure S122. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_CNMF'

P value = 0.00131 (Fisher's exact test), Q value = 0.0029

Table S123. Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 19(10P11.22) MUTATED	43	27	48
AMP PEAK 19(10P11.22) WILD-TYPE	143	106	73

Figure S123. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S124. Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 19(10P11.22) MUTATED	19	34	17	48
AMP PEAK 19(10P11.22) WILD-TYPE	60	141	62	59

Figure S124. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00304 (Fisher's exact test), Q value = 0.0061

Table S125. Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 19(10P11.22) MUTATED	33	14	8	14	12	12
AMP PEAK 19(10P11.22) WILD-TYPE	43	44	52	44	24	46

Figure S125. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.03

Table S126. Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 19(10P11.22) MUTATED	57	11	25
AMP PEAK 19(10P11.22) WILD-TYPE	144	62	47

Figure S126. Get High-res Image Gene #19: 'amp_10p11.22' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

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

Table S127. Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S127. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'METHLYATION_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.06

Table S128. Gene #20: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S128. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10q22.2' versus 'RPPA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.032

Table S129. Gene #20: 'amp_10q22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
AMP PEAK 20(10Q22.2) MUTATED	8	20	23
AMP PEAK 20(10Q22.2) WILD-TYPE	74	70	68

Figure S129. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.026

Table S130. Gene #20: 'amp_10q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 20(10Q22.2) MUTATED	8	10	11	4	21
AMP PEAK 20(10Q22.2) WILD-TYPE	57	52	35	33	41

Figure S130. Get High-res Image Gene #20: 'amp_10q22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.037

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 20(10Q22.2) MUTATED	13	2	7	13	4	13	2
AMP PEAK 20(10Q22.2) WILD-TYPE	25	19	42	49	37	27	19

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

'amp_10q26.13' versus 'CN_CNMF'

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

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

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

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

'amp_10q26.13' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00042

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

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

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

'amp_10q26.13' versus 'RPPA_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.056

Table S134. Gene #21: 'amp_10q26.13' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
AMP PEAK 21(10Q26.13) MUTATED	9	22	22
AMP PEAK 21(10Q26.13) WILD-TYPE	73	68	69

Figure S134. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CNMF'

P value = 0.00637 (Fisher's exact test), Q value = 0.012

Table S135. Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 21(10Q26.13) MUTATED	8	14	5	5	22
AMP PEAK 21(10Q26.13) WILD-TYPE	57	48	41	32	40

Figure S135. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0316 (Fisher's exact test), Q value = 0.05

Table S136. Gene #21: 'amp_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 21(10Q26.13) MUTATED	9	2	10	10	5	16	2
AMP PEAK 21(10Q26.13) WILD-TYPE	29	19	39	52	36	24	19

Figure S136. Get High-res Image Gene #21: 'amp_10q26.13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

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

Table S137. Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S137. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00073

Table S138. Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S138. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

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

Table S139. Gene #22: 'amp_11p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 22(11P13) MUTATED	7	15	5	1	19
AMP PEAK 22(11P13) WILD-TYPE	58	47	41	36	43

Figure S139. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00521 (Fisher's exact test), Q value = 0.0098

Table S140. Gene #22: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 22(11P13) MUTATED	10	4	9	5	4	14	1
AMP PEAK 22(11P13) WILD-TYPE	28	17	40	57	37	26	20

Figure S140. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

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

Table S141. Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 22(11P13) MUTATED	25	21	41
AMP PEAK 22(11P13) WILD-TYPE	161	112	80

Figure S141. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S142. Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 22(11P13) MUTATED	11	25	13	38
AMP PEAK 22(11P13) WILD-TYPE	68	150	66	69

Figure S142. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.052

Table S143. Gene #22: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 22(11P13) MUTATED	23	13	7	6	9	10
AMP PEAK 22(11P13) WILD-TYPE	53	45	53	52	27	48

Figure S143. Get High-res Image Gene #22: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'CN_CNMF'

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

Table S144. Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S144. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

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

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

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

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

'amp_11p11.2' versus 'MRNASEQ_CNMF'

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

Table S146. Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 23(11P11.2) MUTATED	6	8	5	2	24
AMP PEAK 23(11P11.2) WILD-TYPE	59	54	41	35	38

Figure S146. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.00091

Table S147. Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 23(11P11.2) MUTATED	8	3	3	7	6	17	1
AMP PEAK 23(11P11.2) WILD-TYPE	30	18	46	55	35	23	20

Figure S147. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

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

Table S148. Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 23(11P11.2) MUTATED	32	15	44
AMP PEAK 23(11P11.2) WILD-TYPE	154	118	77

Figure S148. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S149. Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 23(11P11.2) MUTATED	14	29	7	41
AMP PEAK 23(11P11.2) WILD-TYPE	65	146	72	66

Figure S149. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00091

Table S150. Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 23(11P11.2) MUTATED	26	16	5	7	9	6
AMP PEAK 23(11P11.2) WILD-TYPE	50	42	55	51	27	52

Figure S150. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.0064

Table S151. Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 23(11P11.2) MUTATED	48	5	16
AMP PEAK 23(11P11.2) WILD-TYPE	153	68	56

Figure S151. Get High-res Image Gene #23: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

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

Table S152. Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S152. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00376 (Fisher's exact test), Q value = 0.0074

Table S153. Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S153. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.059

Table S154. Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 24(11Q13.3) MUTATED	9	4	5	15	9	16	2
AMP PEAK 24(11Q13.3) WILD-TYPE	29	17	44	47	32	24	19

Figure S154. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

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

Table S155. Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 24(11Q13.3) MUTATED	45	20	49
AMP PEAK 24(11Q13.3) WILD-TYPE	141	113	72

Figure S155. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00298 (Fisher's exact test), Q value = 0.0061

Table S156. Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 24(11Q13.3) MUTATED	21	44	10	39
AMP PEAK 24(11Q13.3) WILD-TYPE	58	131	69	68

Figure S156. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0029

Table S157. Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 24(11Q13.3) MUTATED	26	20	7	15	14	8
AMP PEAK 24(11Q13.3) WILD-TYPE	50	38	53	43	22	50

Figure S157. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.072

Table S158. Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 24(11Q13.3) MUTATED	59	11	20
AMP PEAK 24(11Q13.3) WILD-TYPE	142	62	52

Figure S158. Get High-res Image Gene #24: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

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

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

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

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

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.05

Table S160. Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S160. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.057

Table S161. Gene #25: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 25(12P12.1) MUTATED	50	32	46
AMP PEAK 25(12P12.1) WILD-TYPE	136	101	75

Figure S161. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.064

Table S162. Gene #25: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 25(12P12.1) MUTATED	69	14	19
AMP PEAK 25(12P12.1) WILD-TYPE	132	59	53

Figure S162. Get High-res Image Gene #25: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

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

Table S163. Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S163. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

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

Table S164. Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S164. Get High-res Image Gene #26: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

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

Table S165. Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S165. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

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

Table S166. Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S166. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.028

Table S167. Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 27(13Q12.3) MUTATED	21	17	13	19	31
AMP PEAK 27(13Q12.3) WILD-TYPE	44	45	33	18	31

Figure S167. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S168. Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 27(13Q12.3) MUTATED	4	5	17	23	25	22	5
AMP PEAK 27(13Q12.3) WILD-TYPE	34	16	32	39	16	18	16

Figure S168. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

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

Table S169. Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 27(13Q12.3) MUTATED	60	41	68
AMP PEAK 27(13Q12.3) WILD-TYPE	126	92	53

Figure S169. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S170. Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 27(13Q12.3) MUTATED	36	48	25	60
AMP PEAK 27(13Q12.3) WILD-TYPE	43	127	54	47

Figure S170. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00052

Table S171. Gene #27: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 27(13Q12.3) MUTATED	40	16	20	21	21	12
AMP PEAK 27(13Q12.3) WILD-TYPE	36	42	40	37	15	46

Figure S171. Get High-res Image Gene #27: 'amp_13q12.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'CN_CNMF'

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

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

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

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

'amp_13q22.1' versus 'METHLYATION_CNMF'

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

Table S173. Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S173. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

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

Table S174. Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 28(13Q22.1) MUTATED	22	16	9	17	39
AMP PEAK 28(13Q22.1) WILD-TYPE	43	46	37	20	23

Figure S174. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S175. Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 28(13Q22.1) MUTATED	7	6	15	18	24	28	5
AMP PEAK 28(13Q22.1) WILD-TYPE	31	15	34	44	17	12	16

Figure S175. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CNMF'

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

Table S176. Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 28(13Q22.1) MUTATED	64	40	76
AMP PEAK 28(13Q22.1) WILD-TYPE	122	93	45

Figure S176. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S177. Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 28(13Q22.1) MUTATED	37	50	25	68
AMP PEAK 28(13Q22.1) WILD-TYPE	42	125	54	39

Figure S177. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S178. Gene #28: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 28(13Q22.1) MUTATED	46	20	22	21	19	12
AMP PEAK 28(13Q22.1) WILD-TYPE	30	38	38	37	17	46

Figure S178. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0345 (Fisher's exact test), Q value = 0.054

Table S179. Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 28(13Q22.1) MUTATED	92	21	27
AMP PEAK 28(13Q22.1) WILD-TYPE	109	52	45

Figure S179. Get High-res Image Gene #28: 'amp_13q22.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

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

Table S180. Gene #29: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S180. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'METHLYATION_CNMF'

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

Table S181. Gene #29: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S181. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

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

Table S182. Gene #29: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 29(15Q26.1) MUTATED	13	4	10	10	28
AMP PEAK 29(15Q26.1) WILD-TYPE	52	58	36	27	34

Figure S182. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S183. Gene #29: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 29(15Q26.1) MUTATED	13	1	4	13	12	20	2
AMP PEAK 29(15Q26.1) WILD-TYPE	25	20	45	49	29	20	19

Figure S183. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

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

Table S184. Gene #29: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 29(15Q26.1) MUTATED	48	20	44
AMP PEAK 29(15Q26.1) WILD-TYPE	138	113	77

Figure S184. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00073

Table S185. Gene #29: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 29(15Q26.1) MUTATED	20	42	9	41
AMP PEAK 29(15Q26.1) WILD-TYPE	59	133	70	66

Figure S185. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00775 (Fisher's exact test), Q value = 0.014

Table S186. Gene #29: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 29(15Q26.1) MUTATED	29	14	19	18	8	6
AMP PEAK 29(15Q26.1) WILD-TYPE	47	44	41	40	28	52

Figure S186. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.002

Table S187. Gene #29: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 29(15Q26.1) MUTATED	63	8	23
AMP PEAK 29(15Q26.1) WILD-TYPE	138	65	49

Figure S187. Get High-res Image Gene #29: 'amp_15q26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

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

Table S188. Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S188. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

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

Table S189. Gene #30: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S189. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 0.061

Table S190. Gene #30: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
AMP PEAK 30(17Q12) MUTATED	11	30	8	25
AMP PEAK 30(17Q12) WILD-TYPE	23	53	47	66

Figure S190. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S191. Gene #30: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 30(17Q12) MUTATED	14	10	15	8	32
AMP PEAK 30(17Q12) WILD-TYPE	51	52	31	29	30

Figure S191. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S192. Gene #30: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 30(17Q12) MUTATED	13	7	5	20	13	20	1
AMP PEAK 30(17Q12) WILD-TYPE	25	14	44	42	28	20	20

Figure S192. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

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

Table S193. Gene #30: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 30(17Q12) MUTATED	49	28	69
AMP PEAK 30(17Q12) WILD-TYPE	137	105	52

Figure S193. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S194. Gene #30: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 30(17Q12) MUTATED	19	55	17	55
AMP PEAK 30(17Q12) WILD-TYPE	60	120	62	52

Figure S194. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.0085

Table S195. Gene #30: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 30(17Q12) MUTATED	38	17	19	20	11	10
AMP PEAK 30(17Q12) WILD-TYPE	38	41	41	38	25	48

Figure S195. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00064

Table S196. Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 30(17Q12) MUTATED	81	11	23
AMP PEAK 30(17Q12) WILD-TYPE	120	62	49

Figure S196. Get High-res Image Gene #30: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

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

Table S197. Gene #31: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S197. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

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

Table S198. Gene #31: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S198. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.026

Table S199. Gene #31: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 31(18Q11.2) MUTATED	12	12	17	8	25
AMP PEAK 31(18Q11.2) WILD-TYPE	53	50	29	29	37

Figure S199. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0078

Table S200. Gene #31: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 31(18Q11.2) MUTATED	8	2	7	24	11	18	4
AMP PEAK 31(18Q11.2) WILD-TYPE	30	19	42	38	30	22	17

Figure S200. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

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

Table S201. Gene #31: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 31(18Q11.2) MUTATED	49	35	56
AMP PEAK 31(18Q11.2) WILD-TYPE	137	98	65

Figure S201. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0029

Table S202. Gene #31: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 31(18Q11.2) MUTATED	21	48	20	51
AMP PEAK 31(18Q11.2) WILD-TYPE	58	127	59	56

Figure S202. Get High-res Image Gene #31: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

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

Table S203. Gene #32: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S203. Get High-res Image Gene #32: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'CN_CNMF'

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

Table S204. Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S204. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

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

Table S205. Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S205. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.00639 (Fisher's exact test), Q value = 0.012

Table S206. Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
AMP PEAK 33(19Q12) MUTATED	20	18	37
AMP PEAK 33(19Q12) WILD-TYPE	62	72	54

Figure S206. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

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

Table S207. Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 33(19Q12) MUTATED	10	9	10	6	44
AMP PEAK 33(19Q12) WILD-TYPE	55	53	36	31	18

Figure S207. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S208. Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 33(19Q12) MUTATED	10	5	6	15	11	29	3
AMP PEAK 33(19Q12) WILD-TYPE	28	16	43	47	30	11	18

Figure S208. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

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

Table S209. Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 33(19Q12) MUTATED	34	26	69
AMP PEAK 33(19Q12) WILD-TYPE	152	107	52

Figure S209. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S210. Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 33(19Q12) MUTATED	18	27	17	67
AMP PEAK 33(19Q12) WILD-TYPE	61	148	62	40

Figure S210. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

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

Table S211. Gene #33: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 33(19Q12) MUTATED	43	9	15	12	13	12
AMP PEAK 33(19Q12) WILD-TYPE	33	49	45	46	23	46

Figure S211. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.073

Table S212. Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 33(19Q12) MUTATED	69	14	21
AMP PEAK 33(19Q12) WILD-TYPE	132	59	51

Figure S212. Get High-res Image Gene #33: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.32' versus 'CN_CNMF'

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

Table S213. Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S213. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.32' versus 'METHLYATION_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.018

Table S214. Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S214. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.32' versus 'MRNASEQ_CNMF'

P value = 0.00123 (Fisher's exact test), Q value = 0.0028

Table S215. Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 34(19Q13.32) MUTATED	13	8	11	6	27
AMP PEAK 34(19Q13.32) WILD-TYPE	52	54	35	31	35

Figure S215. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_19q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.002

Table S216. Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 34(19Q13.32) MUTATED	38	26	46
AMP PEAK 34(19Q13.32) WILD-TYPE	148	107	75

Figure S216. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00475 (Fisher's exact test), Q value = 0.0091

Table S217. Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 34(19Q13.32) MUTATED	18	36	15	41
AMP PEAK 34(19Q13.32) WILD-TYPE	61	139	64	66

Figure S217. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0051

Table S218. Gene #34: 'amp_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 34(19Q13.32) MUTATED	30	11	8	15	11	8
AMP PEAK 34(19Q13.32) WILD-TYPE	46	47	52	43	25	50

Figure S218. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00872 (Fisher's exact test), Q value = 0.016

Table S219. Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 34(19Q13.32) MUTATED	60	10	13
AMP PEAK 34(19Q13.32) WILD-TYPE	141	63	59

Figure S219. Get High-res Image Gene #34: 'amp_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

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

Table S220. Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S220. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

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

Table S221. Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S221. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

P value = 0.00642 (Fisher's exact test), Q value = 0.012

Table S222. Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
AMP PEAK 35(20Q13.2) MUTATED	49	52	71
AMP PEAK 35(20Q13.2) WILD-TYPE	33	38	20

Figure S222. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

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

Table S223. Gene #35: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
AMP PEAK 35(20Q13.2) MUTATED	22	65	29	56
AMP PEAK 35(20Q13.2) WILD-TYPE	12	18	26	35

Figure S223. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

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

Table S224. Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
AMP PEAK 35(20Q13.2) MUTATED	31	31	31	24	59
AMP PEAK 35(20Q13.2) WILD-TYPE	34	31	15	13	3

Figure S224. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S225. Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 35(20Q13.2) MUTATED	23	19	19	43	31	38	3
AMP PEAK 35(20Q13.2) WILD-TYPE	15	2	30	19	10	2	18

Figure S225. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

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

Table S226. Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
AMP PEAK 35(20Q13.2) MUTATED	107	74	111
AMP PEAK 35(20Q13.2) WILD-TYPE	79	59	10

Figure S226. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S227. Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
AMP PEAK 35(20Q13.2) MUTATED	43	107	41	101
AMP PEAK 35(20Q13.2) WILD-TYPE	36	68	38	6

Figure S227. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S228. Gene #35: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
AMP PEAK 35(20Q13.2) MUTATED	65	30	38	36	26	29
AMP PEAK 35(20Q13.2) WILD-TYPE	11	28	22	22	10	29

Figure S228. Get High-res Image Gene #35: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'amp_xq27.3' versus 'CN_CNMF'

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

Table S229. Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S229. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq27.3' versus 'METHLYATION_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.016

Table S230. Gene #36: 'amp_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S230. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq27.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S231. Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
AMP PEAK 36(XQ27.3) MUTATED	8	4	3	10	19	3	2
AMP PEAK 36(XQ27.3) WILD-TYPE	30	17	46	52	22	37	19

Figure S231. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'amp_xq27.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.026

Table S232. Gene #36: 'amp_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
AMP PEAK 36(XQ27.3) MUTATED	41	6	18
AMP PEAK 36(XQ27.3) WILD-TYPE	160	67	54

Figure S232. Get High-res Image Gene #36: 'amp_xq27.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

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

Table S233. Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S233. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

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

Table S234. Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S234. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.002

Table S235. Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 1(1P36.11) MUTATED	13	36	10	18
DEL PEAK 1(1P36.11) WILD-TYPE	21	47	45	73

Figure S235. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00079

Table S236. Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 1(1P36.11) MUTATED	12	8	17	11	28
DEL PEAK 1(1P36.11) WILD-TYPE	53	54	29	26	34

Figure S236. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S237. Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 1(1P36.11) MUTATED	10	2	4	21	15	22	2
DEL PEAK 1(1P36.11) WILD-TYPE	28	19	45	41	26	18	19

Figure S237. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

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

Table S238. Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 1(1P36.11) MUTATED	53	25	56
DEL PEAK 1(1P36.11) WILD-TYPE	133	108	65

Figure S238. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S239. Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 1(1P36.11) MUTATED	21	45	13	55
DEL PEAK 1(1P36.11) WILD-TYPE	58	130	66	52

Figure S239. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

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

Table S240. Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 1(1P36.11) MUTATED	41	12	19	14	11	8
DEL PEAK 1(1P36.11) WILD-TYPE	35	46	41	44	25	50

Figure S240. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00331 (Fisher's exact test), Q value = 0.0066

Table S241. Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 1(1P36.11) MUTATED	71	11	23
DEL PEAK 1(1P36.11) WILD-TYPE	130	62	49

Figure S241. Get High-res Image Gene #37: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

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

Table S242. Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

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

Figure S242. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

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

Table S243. Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

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

Figure S243. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0022

Table S244. Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 2(1P13.2) MUTATED	8	5	6	8	22
DEL PEAK 2(1P13.2) WILD-TYPE	57	57	40	29	40

Figure S244. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00084 (Fisher's exact test), Q value = 0.002

Table S245. Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 2(1P13.2) MUTATED	7	2	3	11	12	14	0
DEL PEAK 2(1P13.2) WILD-TYPE	31	19	46	51	29	26	21

Figure S245. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.004

Table S246. Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 2(1P13.2) MUTATED	35	19	39
DEL PEAK 2(1P13.2) WILD-TYPE	151	114	82

Figure S246. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00725 (Fisher's exact test), Q value = 0.013

Table S247. Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 2(1P13.2) MUTATED	17	33	9	34
DEL PEAK 2(1P13.2) WILD-TYPE	62	142	70	73

Figure S247. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.027

Table S248. Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 2(1P13.2) MUTATED	53	8	13
DEL PEAK 2(1P13.2) WILD-TYPE	148	65	59

Figure S248. Get High-res Image Gene #38: 'del_1p13.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0013

Table S249. Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 3(1Q44) MUTATED	13	3	6	6	2
DEL PEAK 3(1Q44) WILD-TYPE	110	184	30	70	17

Figure S249. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.0041

Table S250. Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 3(1Q44) MUTATED	16	6	3	1
DEL PEAK 3(1Q44) WILD-TYPE	108	115	39	105

Figure S250. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.044

Table S251. Gene #39: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 3(1Q44) MUTATED	3	2	0	4	5	7	0
DEL PEAK 3(1Q44) WILD-TYPE	35	19	49	58	36	33	21

Figure S251. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00514 (Fisher's exact test), Q value = 0.0097

Table S252. Gene #39: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 3(1Q44) MUTATED	16	2	12
DEL PEAK 3(1Q44) WILD-TYPE	170	131	109

Figure S252. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.029

Table S253. Gene #39: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 3(1Q44) MUTATED	20	1	2
DEL PEAK 3(1Q44) WILD-TYPE	181	72	70

Figure S253. Get High-res Image Gene #39: 'del_1q44' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1q44' versus 'CN_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.0052

Table S254. Gene #40: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 4(1Q44) MUTATED	11	3	4	5	3
DEL PEAK 4(1Q44) WILD-TYPE	112	184	32	71	16

Figure S254. Get High-res Image Gene #40: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0051

Table S255. Gene #40: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 4(1Q44) MUTATED	16	7	2	1
DEL PEAK 4(1Q44) WILD-TYPE	108	114	40	105

Figure S255. Get High-res Image Gene #40: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'CN_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00077

Table S256. Gene #41: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 5(2Q32.1) MUTATED	28	12	7	15	2
DEL PEAK 5(2Q32.1) WILD-TYPE	95	175	29	61	17

Figure S256. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

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

Table S257. Gene #41: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 5(2Q32.1) MUTATED	29	18	1	8
DEL PEAK 5(2Q32.1) WILD-TYPE	95	103	41	98

Figure S257. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MIRSEQ_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.028

Table S258. Gene #41: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 5(2Q32.1) MUTATED	18	20	26
DEL PEAK 5(2Q32.1) WILD-TYPE	168	113	95

Figure S258. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0017

Table S259. Gene #41: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 5(2Q32.1) MUTATED	6	19	10	29
DEL PEAK 5(2Q32.1) WILD-TYPE	73	156	69	78

Figure S259. Get High-res Image Gene #41: 'del_2q32.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00047

Table S260. Gene #42: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 6(2Q33.3) MUTATED	24	8	7	9	1
DEL PEAK 6(2Q33.3) WILD-TYPE	99	179	29	67	18

Figure S260. Get High-res Image Gene #42: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00956 (Fisher's exact test), Q value = 0.017

Table S261. Gene #42: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 6(2Q33.3) MUTATED	6	20	3	20
DEL PEAK 6(2Q33.3) WILD-TYPE	73	155	76	87

Figure S261. Get High-res Image Gene #42: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

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

Table S262. Gene #43: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 7(2Q37.2) MUTATED	36	10	4	15	7
DEL PEAK 7(2Q37.2) WILD-TYPE	87	177	32	61	12

Figure S262. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

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

Table S263. Gene #43: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 7(2Q37.2) MUTATED	38	14	1	14
DEL PEAK 7(2Q37.2) WILD-TYPE	86	107	41	92

Figure S263. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.0056

Table S264. Gene #43: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 7(2Q37.2) MUTATED	3	6	10	6	17
DEL PEAK 7(2Q37.2) WILD-TYPE	62	56	36	31	45

Figure S264. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0029

Table S265. Gene #43: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 7(2Q37.2) MUTATED	23	16	33
DEL PEAK 7(2Q37.2) WILD-TYPE	163	117	88

Figure S265. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S266. Gene #43: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 7(2Q37.2) MUTATED	8	27	4	33
DEL PEAK 7(2Q37.2) WILD-TYPE	71	148	75	74

Figure S266. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.027

Table S267. Gene #43: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 7(2Q37.2) MUTATED	39	5	16
DEL PEAK 7(2Q37.2) WILD-TYPE	162	68	56

Figure S267. Get High-res Image Gene #43: 'del_2q37.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.1' versus 'CN_CNMF'

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

Table S268. Gene #44: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 8(3P26.1) MUTATED	65	19	16	36	7
DEL PEAK 8(3P26.1) WILD-TYPE	58	168	20	40	12

Figure S268. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.1' versus 'METHLYATION_CNMF'

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

Table S269. Gene #44: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 8(3P26.1) MUTATED	67	33	9	20
DEL PEAK 8(3P26.1) WILD-TYPE	57	88	33	86

Figure S269. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.1' versus 'MRNASEQ_CNMF'

P value = 0.00619 (Fisher's exact test), Q value = 0.011

Table S270. Gene #44: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 8(3P26.1) MUTATED	11	11	14	13	26
DEL PEAK 8(3P26.1) WILD-TYPE	54	51	32	24	36

Figure S270. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p26.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S271. Gene #44: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 8(3P26.1) MUTATED	8	5	8	16	20	18	0
DEL PEAK 8(3P26.1) WILD-TYPE	30	16	41	46	21	22	21

Figure S271. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_CNMF'

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

Table S272. Gene #44: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 8(3P26.1) MUTATED	50	32	60
DEL PEAK 8(3P26.1) WILD-TYPE	136	101	61

Figure S272. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p26.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S273. Gene #44: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 8(3P26.1) MUTATED	22	45	17	58
DEL PEAK 8(3P26.1) WILD-TYPE	57	130	62	49

Figure S273. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S274. Gene #44: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 8(3P26.1) MUTATED	40	18	14	13	16	11
DEL PEAK 8(3P26.1) WILD-TYPE	36	40	46	45	20	47

Figure S274. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0055 (Fisher's exact test), Q value = 0.01

Table S275. Gene #44: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 8(3P26.1) MUTATED	78	14	20
DEL PEAK 8(3P26.1) WILD-TYPE	123	59	52

Figure S275. Get High-res Image Gene #44: 'del_3p26.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

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

Table S276. Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 9(3P14.2) MUTATED	67	28	16	37	10
DEL PEAK 9(3P14.2) WILD-TYPE	56	159	20	39	9

Figure S276. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

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

Table S277. Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 9(3P14.2) MUTATED	70	41	15	19
DEL PEAK 9(3P14.2) WILD-TYPE	54	80	27	87

Figure S277. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

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

Table S278. Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 9(3P14.2) MUTATED	16	10	15	13	34
DEL PEAK 9(3P14.2) WILD-TYPE	49	52	31	24	28

Figure S278. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.00073

Table S279. Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 9(3P14.2) MUTATED	11	6	6	21	19	22	3
DEL PEAK 9(3P14.2) WILD-TYPE	27	15	43	41	22	18	18

Figure S279. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

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

Table S280. Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 9(3P14.2) MUTATED	61	32	65
DEL PEAK 9(3P14.2) WILD-TYPE	125	101	56

Figure S280. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S281. Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 9(3P14.2) MUTATED	27	52	18	61
DEL PEAK 9(3P14.2) WILD-TYPE	52	123	61	46

Figure S281. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00424 (Fisher's exact test), Q value = 0.0082

Table S282. Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 9(3P14.2) MUTATED	40	20	22	19	13	11
DEL PEAK 9(3P14.2) WILD-TYPE	36	38	38	39	23	47

Figure S282. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00059

Table S283. Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 9(3P14.2) MUTATED	84	12	29
DEL PEAK 9(3P14.2) WILD-TYPE	117	61	43

Figure S283. Get High-res Image Gene #45: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

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

Table S284. Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 10(3Q26.31) MUTATED	27	3	6	10	1
DEL PEAK 10(3Q26.31) WILD-TYPE	96	184	30	66	18

Figure S284. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

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

Table S285. Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 10(3Q26.31) MUTATED	28	11	2	2
DEL PEAK 10(3Q26.31) WILD-TYPE	96	110	40	104

Figure S285. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'RPPA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.054

Table S286. Gene #46: 'del_3q26.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 10(3Q26.31) MUTATED	10	3	12
DEL PEAK 10(3Q26.31) WILD-TYPE	72	87	79

Figure S286. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_3q26.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.072

Table S287. Gene #46: 'del_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 10(3Q26.31) MUTATED	4	12	6	3
DEL PEAK 10(3Q26.31) WILD-TYPE	30	71	49	88

Figure S287. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_3q26.31' versus 'MRNASEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0013

Table S288. Gene #46: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 10(3Q26.31) MUTATED	2	3	1	5	14
DEL PEAK 10(3Q26.31) WILD-TYPE	63	59	45	32	48

Figure S288. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S289. Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 10(3Q26.31) MUTATED	3	1	1	1	10	9	0
DEL PEAK 10(3Q26.31) WILD-TYPE	35	20	48	61	31	31	21

Figure S289. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CNMF'

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

Table S290. Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 10(3Q26.31) MUTATED	12	8	27
DEL PEAK 10(3Q26.31) WILD-TYPE	174	125	94

Figure S290. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.005 (Fisher's exact test), Q value = 0.0095

Table S291. Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 10(3Q26.31) MUTATED	6	14	5	22
DEL PEAK 10(3Q26.31) WILD-TYPE	73	161	74	85

Figure S291. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00432 (Fisher's exact test), Q value = 0.0083

Table S292. Gene #46: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 10(3Q26.31) MUTATED	16	5	3	4	7	2
DEL PEAK 10(3Q26.31) WILD-TYPE	60	53	57	54	29	56

Figure S292. Get High-res Image Gene #46: 'del_3q26.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'CN_CNMF'

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

Table S293. Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 11(4P16.3) MUTATED	76	33	12	44	4
DEL PEAK 11(4P16.3) WILD-TYPE	47	154	24	32	15

Figure S293. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

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

Table S294. Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 11(4P16.3) MUTATED	70	39	6	35
DEL PEAK 11(4P16.3) WILD-TYPE	54	82	36	71

Figure S294. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

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

Table S295. Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 11(4P16.3) MUTATED	11	23	15	11	38
DEL PEAK 11(4P16.3) WILD-TYPE	54	39	31	26	24

Figure S295. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S296. Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 11(4P16.3) MUTATED	10	4	18	18	17	28	3
DEL PEAK 11(4P16.3) WILD-TYPE	28	17	31	44	24	12	18

Figure S296. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

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

Table S297. Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 11(4P16.3) MUTATED	53	49	67
DEL PEAK 11(4P16.3) WILD-TYPE	133	84	54

Figure S297. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S298. Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 11(4P16.3) MUTATED	23	49	27	70
DEL PEAK 11(4P16.3) WILD-TYPE	56	126	52	37

Figure S298. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00079

Table S299. Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 11(4P16.3) MUTATED	44	20	13	17	17	24
DEL PEAK 11(4P16.3) WILD-TYPE	32	38	47	41	19	34

Figure S299. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.021

Table S300. Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 11(4P16.3) MUTATED	91	25	19
DEL PEAK 11(4P16.3) WILD-TYPE	110	48	53

Figure S300. Get High-res Image Gene #47: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

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

Table S301. Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 12(4Q22.1) MUTATED	83	30	17	55	8
DEL PEAK 12(4Q22.1) WILD-TYPE	40	157	19	21	11

Figure S301. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

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

Table S302. Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 12(4Q22.1) MUTATED	77	52	6	37
DEL PEAK 12(4Q22.1) WILD-TYPE	47	69	36	69

Figure S302. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00241 (Fisher's exact test), Q value = 0.005

Table S303. Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 12(4Q22.1) MUTATED	19	20	20	17	38
DEL PEAK 12(4Q22.1) WILD-TYPE	46	42	26	20	24

Figure S303. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S304. Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 12(4Q22.1) MUTATED	16	4	16	23	25	27	3
DEL PEAK 12(4Q22.1) WILD-TYPE	22	17	33	39	16	13	18

Figure S304. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.002

Table S305. Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 12(4Q22.1) MUTATED	71	51	70
DEL PEAK 12(4Q22.1) WILD-TYPE	115	82	51

Figure S305. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S306. Gene #48: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 12(4Q22.1) MUTATED	30	70	27	65
DEL PEAK 12(4Q22.1) WILD-TYPE	49	105	52	42

Figure S306. Get High-res Image Gene #48: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

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

Table S307. Gene #49: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 13(4Q34.3) MUTATED	88	31	14	59	8
DEL PEAK 13(4Q34.3) WILD-TYPE	35	156	22	17	11

Figure S307. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

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

Table S308. Gene #49: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 13(4Q34.3) MUTATED	86	49	4	42
DEL PEAK 13(4Q34.3) WILD-TYPE	38	72	38	64

Figure S308. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00872 (Fisher's exact test), Q value = 0.016

Table S309. Gene #49: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 13(4Q34.3) MUTATED	13	45	14	40
DEL PEAK 13(4Q34.3) WILD-TYPE	21	38	41	51

Figure S309. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

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

Table S310. Gene #49: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 13(4Q34.3) MUTATED	14	21	21	16	41
DEL PEAK 13(4Q34.3) WILD-TYPE	51	41	25	21	21

Figure S310. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S311. Gene #49: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 13(4Q34.3) MUTATED	16	2	17	23	21	30	4
DEL PEAK 13(4Q34.3) WILD-TYPE	22	19	32	39	20	10	17

Figure S311. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

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

Table S312. Gene #49: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 13(4Q34.3) MUTATED	68	48	84
DEL PEAK 13(4Q34.3) WILD-TYPE	118	85	37

Figure S312. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S313. Gene #49: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 13(4Q34.3) MUTATED	29	70	27	74
DEL PEAK 13(4Q34.3) WILD-TYPE	50	105	52	33

Figure S313. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.022

Table S314. Gene #49: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 13(4Q34.3) MUTATED	48	27	21	24	19	22
DEL PEAK 13(4Q34.3) WILD-TYPE	28	31	39	34	17	36

Figure S314. Get High-res Image Gene #49: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'CN_CNMF'

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

Table S315. Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 14(5Q12.1) MUTATED	92	16	11	41	10
DEL PEAK 14(5Q12.1) WILD-TYPE	31	171	25	35	9

Figure S315. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

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

Table S316. Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 14(5Q12.1) MUTATED	92	39	4	21
DEL PEAK 14(5Q12.1) WILD-TYPE	32	82	38	85

Figure S316. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

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

Table S317. Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 14(5Q12.1) MUTATED	17	5	11	14	44
DEL PEAK 14(5Q12.1) WILD-TYPE	48	57	35	23	18

Figure S317. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S318. Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 14(5Q12.1) MUTATED	13	4	3	23	18	28	2
DEL PEAK 14(5Q12.1) WILD-TYPE	25	17	46	39	23	12	19

Figure S318. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

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

Table S319. Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 14(5Q12.1) MUTATED	60	27	83
DEL PEAK 14(5Q12.1) WILD-TYPE	126	106	38

Figure S319. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S320. Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 14(5Q12.1) MUTATED	26	55	11	78
DEL PEAK 14(5Q12.1) WILD-TYPE	53	120	68	29

Figure S320. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S321. Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 14(5Q12.1) MUTATED	52	22	22	19	15	11
DEL PEAK 14(5Q12.1) WILD-TYPE	24	36	38	39	21	47

Figure S321. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S322. Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 14(5Q12.1) MUTATED	100	14	27
DEL PEAK 14(5Q12.1) WILD-TYPE	101	59	45

Figure S322. Get High-res Image Gene #50: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q23.2' versus 'CN_CNMF'

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

Table S323. Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 15(5Q23.2) MUTATED	90	12	11	35	10
DEL PEAK 15(5Q23.2) WILD-TYPE	33	175	25	41	9

Figure S323. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q23.2' versus 'METHLYATION_CNMF'

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

Table S324. Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 15(5Q23.2) MUTATED	88	34	6	17
DEL PEAK 15(5Q23.2) WILD-TYPE	36	87	36	89

Figure S324. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_5q23.2' versus 'MRNASEQ_CNMF'

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

Table S325. Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 15(5Q23.2) MUTATED	15	3	10	12	43
DEL PEAK 15(5Q23.2) WILD-TYPE	50	59	36	25	19

Figure S325. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q23.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S326. Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 15(5Q23.2) MUTATED	7	5	2	21	18	28	2
DEL PEAK 15(5Q23.2) WILD-TYPE	31	16	47	41	23	12	19

Figure S326. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_CNMF'

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

Table S327. Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 15(5Q23.2) MUTATED	54	22	81
DEL PEAK 15(5Q23.2) WILD-TYPE	132	111	40

Figure S327. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_5q23.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S328. Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 15(5Q23.2) MUTATED	22	54	10	71
DEL PEAK 15(5Q23.2) WILD-TYPE	57	121	69	36

Figure S328. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_5q23.2' versus 'MIRSEQ_MATURE_CNMF'

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

Table S329. Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 15(5Q23.2) MUTATED	53	20	16	17	14	10
DEL PEAK 15(5Q23.2) WILD-TYPE	23	38	44	41	22	48

Figure S329. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_5q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330. Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 15(5Q23.2) MUTATED	93	12	25
DEL PEAK 15(5Q23.2) WILD-TYPE	108	61	47

Figure S330. Get High-res Image Gene #51: 'del_5q23.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

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

Table S331. Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 16(6P25.3) MUTATED	51	21	8	30	5
DEL PEAK 16(6P25.3) WILD-TYPE	72	166	28	46	14

Figure S331. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

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

Table S332. Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 16(6P25.3) MUTATED	54	33	3	18
DEL PEAK 16(6P25.3) WILD-TYPE	70	88	39	88

Figure S332. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

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

Table S333. Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 16(6P25.3) MUTATED	7	6	14	6	24
DEL PEAK 16(6P25.3) WILD-TYPE	58	56	32	31	38

Figure S333. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S334. Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 16(6P25.3) MUTATED	10	0	4	15	9	18	1
DEL PEAK 16(6P25.3) WILD-TYPE	28	21	45	47	32	22	20

Figure S334. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

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

Table S335. Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 16(6P25.3) MUTATED	40	24	51
DEL PEAK 16(6P25.3) WILD-TYPE	146	109	70

Figure S335. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S336. Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 16(6P25.3) MUTATED	12	47	10	46
DEL PEAK 16(6P25.3) WILD-TYPE	67	128	69	61

Figure S336. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0466 (Fisher's exact test), Q value = 0.071

Table S337. Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 16(6P25.3) MUTATED	58	12	24
DEL PEAK 16(6P25.3) WILD-TYPE	143	61	48

Figure S337. Get High-res Image Gene #52: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q14.1' versus 'CN_CNMF'

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

Table S338. Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 17(6Q14.1) MUTATED	30	13	10	30	6
DEL PEAK 17(6Q14.1) WILD-TYPE	93	174	26	46	13

Figure S338. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q14.1' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00055

Table S339. Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 17(6Q14.1) MUTATED	41	20	3	15
DEL PEAK 17(6Q14.1) WILD-TYPE	83	101	39	91

Figure S339. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q14.1' versus 'MRNASEQ_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S340. Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 17(6Q14.1) MUTATED	7	4	17	6	14
DEL PEAK 17(6Q14.1) WILD-TYPE	58	58	29	31	48

Figure S340. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00439 (Fisher's exact test), Q value = 0.0085

Table S341. Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 17(6Q14.1) MUTATED	5	2	3	18	5	13	2
DEL PEAK 17(6Q14.1) WILD-TYPE	33	19	46	44	36	27	19

Figure S341. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00089 (Fisher's exact test), Q value = 0.002

Table S342. Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 17(6Q14.1) MUTATED	8	44	8	29
DEL PEAK 17(6Q14.1) WILD-TYPE	71	131	71	78

Figure S342. Get High-res Image Gene #53: 'del_6q14.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q24.3' versus 'CN_CNMF'

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

Table S343. Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 18(6Q24.3) MUTATED	26	11	11	24	6
DEL PEAK 18(6Q24.3) WILD-TYPE	97	176	25	52	13

Figure S343. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q24.3' versus 'METHLYATION_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.004

Table S344. Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 18(6Q24.3) MUTATED	35	15	3	15
DEL PEAK 18(6Q24.3) WILD-TYPE	89	106	39	91

Figure S344. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.024

Table S345. Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 18(6Q24.3) MUTATED	6	4	10	5	16
DEL PEAK 18(6Q24.3) WILD-TYPE	59	58	36	32	46

Figure S345. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.037

Table S346. Gene #54: 'del_6q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 18(6Q24.3) MUTATED	4	2	3	11	7	13	1
DEL PEAK 18(6Q24.3) WILD-TYPE	34	19	46	51	34	27	20

Figure S346. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.049

Table S347. Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 18(6Q24.3) MUTATED	10	35	7	25
DEL PEAK 18(6Q24.3) WILD-TYPE	69	140	72	82

Figure S347. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.024

Table S348. Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 18(6Q24.3) MUTATED	18	16	8	9	5	3
DEL PEAK 18(6Q24.3) WILD-TYPE	58	42	52	49	31	55

Figure S348. Get High-res Image Gene #54: 'del_6q24.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'CN_CNMF'

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

Table S349. Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 19(6Q26) MUTATED	36	21	12	29	4
DEL PEAK 19(6Q26) WILD-TYPE	87	166	24	47	15

Figure S349. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.054

Table S350. Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 19(6Q26) MUTATED	40	24	6	21
DEL PEAK 19(6Q26) WILD-TYPE	84	97	36	85

Figure S350. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.0019

Table S351. Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 19(6Q26) MUTATED	13	5	16	4	20
DEL PEAK 19(6Q26) WILD-TYPE	52	57	30	33	42

Figure S351. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0045

Table S352. Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 19(6Q26) MUTATED	12	3	3	17	8	14	1
DEL PEAK 19(6Q26) WILD-TYPE	26	18	46	45	33	26	20

Figure S352. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.063

Table S353. Gene #55: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 19(6Q26) MUTATED	39	25	38
DEL PEAK 19(6Q26) WILD-TYPE	147	108	83

Figure S353. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00731 (Fisher's exact test), Q value = 0.013

Table S354. Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 19(6Q26) MUTATED	14	47	9	32
DEL PEAK 19(6Q26) WILD-TYPE	65	128	70	75

Figure S354. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00299 (Fisher's exact test), Q value = 0.0061

Table S355. Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 19(6Q26) MUTATED	21	19	14	14	6	3
DEL PEAK 19(6Q26) WILD-TYPE	55	39	46	44	30	55

Figure S355. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00213 (Fisher's exact test), Q value = 0.0045

Table S356. Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 19(6Q26) MUTATED	57	7	13
DEL PEAK 19(6Q26) WILD-TYPE	144	66	59

Figure S356. Get High-res Image Gene #55: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

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

Table S357. Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 20(7Q31.1) MUTATED	33	10	1	23	4
DEL PEAK 20(7Q31.1) WILD-TYPE	90	177	35	53	15

Figure S357. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0015

Table S358. Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 20(7Q31.1) MUTATED	30	23	3	7
DEL PEAK 20(7Q31.1) WILD-TYPE	94	98	39	99

Figure S358. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00919 (Fisher's exact test), Q value = 0.016

Table S359. Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 20(7Q31.1) MUTATED	5	8	5	5	19
DEL PEAK 20(7Q31.1) WILD-TYPE	60	54	41	32	43

Figure S359. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0017

Table S360. Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 20(7Q31.1) MUTATED	26	12	32
DEL PEAK 20(7Q31.1) WILD-TYPE	160	121	89

Figure S360. Get High-res Image Gene #56: 'del_7q31.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'CN_CNMF'

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

Table S361. Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 21(7Q36.3) MUTATED	50	8	1	31	8
DEL PEAK 21(7Q36.3) WILD-TYPE	73	179	35	45	11

Figure S361. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

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

Table S362. Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 21(7Q36.3) MUTATED	46	29	0	14
DEL PEAK 21(7Q36.3) WILD-TYPE	78	92	42	92

Figure S362. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

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

Table S363. Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 21(7Q36.3) MUTATED	7	8	8	3	27
DEL PEAK 21(7Q36.3) WILD-TYPE	58	54	38	34	35

Figure S363. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.001

Table S364. Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 21(7Q36.3) MUTATED	12	0	6	13	7	15	0
DEL PEAK 21(7Q36.3) WILD-TYPE	26	21	43	49	34	25	21

Figure S364. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

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

Table S365. Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 21(7Q36.3) MUTATED	36	14	48
DEL PEAK 21(7Q36.3) WILD-TYPE	150	119	73

Figure S365. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S366. Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 21(7Q36.3) MUTATED	14	33	7	44
DEL PEAK 21(7Q36.3) WILD-TYPE	65	142	72	63

Figure S366. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00338 (Fisher's exact test), Q value = 0.0068

Table S367. Gene #57: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 21(7Q36.3) MUTATED	30	10	13	14	10	6
DEL PEAK 21(7Q36.3) WILD-TYPE	46	48	47	44	26	52

Figure S367. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00816 (Fisher's exact test), Q value = 0.015

Table S368. Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 21(7Q36.3) MUTATED	56	8	19
DEL PEAK 21(7Q36.3) WILD-TYPE	145	65	53

Figure S368. Get High-res Image Gene #57: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.3' versus 'CN_CNMF'

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

Table S369. Gene #58: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 22(8P23.3) MUTATED	61	16	16	33	0
DEL PEAK 22(8P23.3) WILD-TYPE	62	171	20	43	19

Figure S369. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.3' versus 'METHLYATION_CNMF'

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

Table S370. Gene #58: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 22(8P23.3) MUTATED	61	27	3	22
DEL PEAK 22(8P23.3) WILD-TYPE	63	94	39	84

Figure S370. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.3' versus 'MRNASEQ_CNMF'

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

Table S371. Gene #58: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 22(8P23.3) MUTATED	11	9	8	10	34
DEL PEAK 22(8P23.3) WILD-TYPE	54	53	38	27	28

Figure S371. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_8p23.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S372. Gene #58: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 22(8P23.3) MUTATED	9	2	6	13	15	25	2
DEL PEAK 22(8P23.3) WILD-TYPE	29	19	43	49	26	15	19

Figure S372. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_CNMF'

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

Table S373. Gene #58: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 22(8P23.3) MUTATED	45	25	55
DEL PEAK 22(8P23.3) WILD-TYPE	141	108	66

Figure S373. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_8p23.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S374. Gene #58: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 22(8P23.3) MUTATED	21	40	14	50
DEL PEAK 22(8P23.3) WILD-TYPE	58	135	65	57

Figure S374. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00895 (Fisher's exact test), Q value = 0.016

Table S375. Gene #58: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 22(8P23.3) MUTATED	36	14	16	13	10	12
DEL PEAK 22(8P23.3) WILD-TYPE	40	44	44	45	26	46

Figure S375. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_8p23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00024

Table S376. Gene #58: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 22(8P23.3) MUTATED	74	8	19
DEL PEAK 22(8P23.3) WILD-TYPE	127	65	53

Figure S376. Get High-res Image Gene #58: 'del_8p23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

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

Table S377. Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 23(9P23) MUTATED	72	27	23	61	12
DEL PEAK 23(9P23) WILD-TYPE	51	160	13	15	7

Figure S377. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

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

Table S378. Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 23(9P23) MUTATED	84	46	9	37
DEL PEAK 23(9P23) WILD-TYPE	40	75	33	69

Figure S378. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.0295 (Fisher's exact test), Q value = 0.047

Table S379. Gene #59: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 23(9P23) MUTATED	25	38	46
DEL PEAK 23(9P23) WILD-TYPE	57	52	45

Figure S379. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0023

Table S380. Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 23(9P23) MUTATED	12	41	11	45
DEL PEAK 23(9P23) WILD-TYPE	22	42	44	46

Figure S380. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

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

Table S381. Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 23(9P23) MUTATED	14	18	23	13	40
DEL PEAK 23(9P23) WILD-TYPE	51	44	23	24	22

Figure S381. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00213 (Fisher's exact test), Q value = 0.0045

Table S382. Gene #59: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 23(9P23) MUTATED	18	5	14	28	18	23	2
DEL PEAK 23(9P23) WILD-TYPE	20	16	35	34	23	17	19

Figure S382. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

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

Table S383. Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 23(9P23) MUTATED	68	51	75
DEL PEAK 23(9P23) WILD-TYPE	118	82	46

Figure S383. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 5e-04

Table S384. Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 23(9P23) MUTATED	27	72	28	67
DEL PEAK 23(9P23) WILD-TYPE	52	103	51	40

Figure S384. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00365 (Fisher's exact test), Q value = 0.0073

Table S385. Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 23(9P23) MUTATED	103	21	31
DEL PEAK 23(9P23) WILD-TYPE	98	52	41

Figure S385. Get High-res Image Gene #59: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

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

Table S386. Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 24(9P21.3) MUTATED	73	29	21	59	11
DEL PEAK 24(9P21.3) WILD-TYPE	50	158	15	17	8

Figure S386. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

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

Table S387. Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 24(9P21.3) MUTATED	90	47	1	37
DEL PEAK 24(9P21.3) WILD-TYPE	34	74	41	69

Figure S387. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'RPPA_CNMF'

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

Table S388. Gene #60: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 24(9P21.3) MUTATED	17	41	47
DEL PEAK 24(9P21.3) WILD-TYPE	65	49	44

Figure S388. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_9p21.3' versus 'RPPA_CHIERARCHICAL'

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

Table S389. Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 24(9P21.3) MUTATED	8	45	10	42
DEL PEAK 24(9P21.3) WILD-TYPE	26	38	45	49

Figure S389. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_9p21.3' versus 'MRNASEQ_CNMF'

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

Table S390. Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 24(9P21.3) MUTATED	9	18	23	15	43
DEL PEAK 24(9P21.3) WILD-TYPE	56	44	23	22	19

Figure S390. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S391. Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 24(9P21.3) MUTATED	19	1	11	30	18	27	2
DEL PEAK 24(9P21.3) WILD-TYPE	19	20	38	32	23	13	19

Figure S391. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

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

Table S392. Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 24(9P21.3) MUTATED	65	50	77
DEL PEAK 24(9P21.3) WILD-TYPE	121	83	44

Figure S392. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S393. Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 24(9P21.3) MUTATED	25	71	27	69
DEL PEAK 24(9P21.3) WILD-TYPE	54	104	52	38

Figure S393. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.046

Table S394. Gene #60: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 24(9P21.3) MUTATED	45	25	23	21	20	21
DEL PEAK 24(9P21.3) WILD-TYPE	31	33	37	37	16	37

Figure S394. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.05

Table S395. Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 24(9P21.3) MUTATED	101	24	30
DEL PEAK 24(9P21.3) WILD-TYPE	100	49	42

Figure S395. Get High-res Image Gene #60: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

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

Table S396. Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 25(9Q21.11) MUTATED	48	12	12	37	5
DEL PEAK 25(9Q21.11) WILD-TYPE	75	175	24	39	14

Figure S396. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

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

Table S397. Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 25(9Q21.11) MUTATED	53	26	2	24
DEL PEAK 25(9Q21.11) WILD-TYPE	71	95	40	82

Figure S397. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.00156 (Fisher's exact test), Q value = 0.0034

Table S398. Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 25(9Q21.11) MUTATED	8	12	13	6	26
DEL PEAK 25(9Q21.11) WILD-TYPE	57	50	33	31	36

Figure S398. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0361 (Fisher's exact test), Q value = 0.056

Table S399. Gene #61: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 25(9Q21.11) MUTATED	7	2	10	18	9	17	2
DEL PEAK 25(9Q21.11) WILD-TYPE	31	19	39	44	32	23	19

Figure S399. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

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

Table S400. Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 25(9Q21.11) MUTATED	34	29	51
DEL PEAK 25(9Q21.11) WILD-TYPE	152	104	70

Figure S400. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S401. Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 25(9Q21.11) MUTATED	13	34	17	50
DEL PEAK 25(9Q21.11) WILD-TYPE	66	141	62	57

Figure S401. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.057

Table S402. Gene #61: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 25(9Q21.11) MUTATED	32	12	12	13	11	14
DEL PEAK 25(9Q21.11) WILD-TYPE	44	46	48	45	25	44

Figure S402. Get High-res Image Gene #61: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10p12.31' versus 'CN_CNMF'

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

Table S403. Gene #62: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 26(10P12.31) MUTATED	34	11	3	12	7
DEL PEAK 26(10P12.31) WILD-TYPE	89	176	33	64	12

Figure S403. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p12.31' versus 'METHLYATION_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.004

Table S404. Gene #62: 'del_10p12.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 26(10P12.31) MUTATED	31	15	2	11
DEL PEAK 26(10P12.31) WILD-TYPE	93	106	40	95

Figure S404. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p12.31' versus 'MIRSEQ_CNMF'

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

Table S405. Gene #62: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 26(10P12.31) MUTATED	23	10	34
DEL PEAK 26(10P12.31) WILD-TYPE	163	123	87

Figure S405. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10p12.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.0035

Table S406. Gene #62: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 26(10P12.31) MUTATED	11	28	3	25
DEL PEAK 26(10P12.31) WILD-TYPE	68	147	76	82

Figure S406. Get High-res Image Gene #62: 'del_10p12.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

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

Table S407. Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 27(10Q22.3) MUTATED	46	8	11	8	6
DEL PEAK 27(10Q22.3) WILD-TYPE	77	179	25	68	13

Figure S407. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 5e-04

Table S408. Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 27(10Q22.3) MUTATED	38	15	3	14
DEL PEAK 27(10Q22.3) WILD-TYPE	86	106	39	92

Figure S408. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00069

Table S409. Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 27(10Q22.3) MUTATED	8	2	4	8	19
DEL PEAK 27(10Q22.3) WILD-TYPE	57	60	42	29	43

Figure S409. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00057 (Fisher's exact test), Q value = 0.0014

Table S410. Gene #63: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 27(10Q22.3) MUTATED	2	2	3	8	14	11	1
DEL PEAK 27(10Q22.3) WILD-TYPE	36	19	46	54	27	29	20

Figure S410. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_CNMF'

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

Table S411. Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 27(10Q22.3) MUTATED	34	10	35
DEL PEAK 27(10Q22.3) WILD-TYPE	152	123	86

Figure S411. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S412. Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 27(10Q22.3) MUTATED	18	21	6	34
DEL PEAK 27(10Q22.3) WILD-TYPE	61	154	73	73

Figure S412. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.045

Table S413. Gene #63: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 27(10Q22.3) MUTATED	23	7	8	7	6	6
DEL PEAK 27(10Q22.3) WILD-TYPE	53	51	52	51	30	52

Figure S413. Get High-res Image Gene #63: 'del_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'CN_CNMF'

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

Table S414. Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 28(10Q23.31) MUTATED	66	13	11	18	8
DEL PEAK 28(10Q23.31) WILD-TYPE	57	174	25	58	11

Figure S414. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

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

Table S415. Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 28(10Q23.31) MUTATED	57	24	4	17
DEL PEAK 28(10Q23.31) WILD-TYPE	67	97	38	89

Figure S415. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00064

Table S416. Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 28(10Q23.31) MUTATED	7	34	8	13
DEL PEAK 28(10Q23.31) WILD-TYPE	27	49	47	78

Figure S416. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

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

Table S417. Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 28(10Q23.31) MUTATED	8	4	9	12	28
DEL PEAK 28(10Q23.31) WILD-TYPE	57	58	37	25	34

Figure S417. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S418. Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 28(10Q23.31) MUTATED	2	3	4	16	18	17	1
DEL PEAK 28(10Q23.31) WILD-TYPE	36	18	45	46	23	23	20

Figure S418. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

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

Table S419. Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 28(10Q23.31) MUTATED	51	17	48
DEL PEAK 28(10Q23.31) WILD-TYPE	135	116	73

Figure S419. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S420. Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 28(10Q23.31) MUTATED	21	39	9	47
DEL PEAK 28(10Q23.31) WILD-TYPE	58	136	70	60

Figure S420. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0042

Table S421. Gene #64: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 28(10Q23.31) MUTATED	33	11	12	14	11	8
DEL PEAK 28(10Q23.31) WILD-TYPE	43	47	48	44	25	50

Figure S421. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0487 (Fisher's exact test), Q value = 0.073

Table S422. Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 28(10Q23.31) MUTATED	56	11	22
DEL PEAK 28(10Q23.31) WILD-TYPE	145	62	50

Figure S422. Get High-res Image Gene #64: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

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

Table S423. Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 29(11P15.5) MUTATED	51	10	8	27	1
DEL PEAK 29(11P15.5) WILD-TYPE	72	177	28	49	18

Figure S423. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

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

Table S424. Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 29(11P15.5) MUTATED	46	22	2	13
DEL PEAK 29(11P15.5) WILD-TYPE	78	99	40	93

Figure S424. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

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

Table S425. Gene #65: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 29(11P15.5) MUTATED	7	15	33
DEL PEAK 29(11P15.5) WILD-TYPE	75	75	58

Figure S425. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00516 (Fisher's exact test), Q value = 0.0097

Table S426. Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 29(11P15.5) MUTATED	2	27	8	18
DEL PEAK 29(11P15.5) WILD-TYPE	32	56	47	73

Figure S426. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.0073

Table S427. Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 29(11P15.5) MUTATED	7	6	6	7	21
DEL PEAK 29(11P15.5) WILD-TYPE	58	56	40	30	41

Figure S427. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.049

Table S428. Gene #65: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 29(11P15.5) MUTATED	7	2	6	9	7	15	1
DEL PEAK 29(11P15.5) WILD-TYPE	31	19	43	53	34	25	20

Figure S428. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

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

Table S429. Gene #65: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 29(11P15.5) MUTATED	33	20	44
DEL PEAK 29(11P15.5) WILD-TYPE	153	113	77

Figure S429. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.0031

Table S430. Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 29(11P15.5) MUTATED	10	40	11	36
DEL PEAK 29(11P15.5) WILD-TYPE	69	135	68	71

Figure S430. Get High-res Image Gene #65: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

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

Table S431. Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 30(11Q23.2) MUTATED	42	18	7	28	4
DEL PEAK 30(11Q23.2) WILD-TYPE	81	169	29	48	15

Figure S431. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0022

Table S432. Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 30(11Q23.2) MUTATED	42	23	3	21
DEL PEAK 30(11Q23.2) WILD-TYPE	82	98	39	85

Figure S432. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 0.00099 (Fisher's exact test), Q value = 0.0022

Table S433. Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 30(11Q23.2) MUTATED	5	8	17	9	16
DEL PEAK 30(11Q23.2) WILD-TYPE	60	54	29	28	46

Figure S433. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S434. Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 30(11Q23.2) MUTATED	4	1	7	24	7	12	0
DEL PEAK 30(11Q23.2) WILD-TYPE	34	20	42	38	34	28	21

Figure S434. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.047

Table S435. Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 30(11Q23.2) MUTATED	25	10	14	16	3	9
DEL PEAK 30(11Q23.2) WILD-TYPE	51	48	46	42	33	49

Figure S435. Get High-res Image Gene #66: 'del_11q23.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_12p13.1' versus 'CN_CNMF'

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

Table S436. Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 31(12P13.1) MUTATED	46	6	6	12	7
DEL PEAK 31(12P13.1) WILD-TYPE	77	181	30	64	12

Figure S436. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

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

Table S437. Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 31(12P13.1) MUTATED	47	16	1	5
DEL PEAK 31(12P13.1) WILD-TYPE	77	105	41	101

Figure S437. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CNMF'

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

Table S438. Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 31(12P13.1) MUTATED	4	5	5	4	23
DEL PEAK 31(12P13.1) WILD-TYPE	61	57	41	33	39

Figure S438. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S439. Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 31(12P13.1) MUTATED	7	0	3	8	6	17	0
DEL PEAK 31(12P13.1) WILD-TYPE	31	21	46	54	35	23	21

Figure S439. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00091

Table S440. Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 31(12P13.1) MUTATED	29	13	35
DEL PEAK 31(12P13.1) WILD-TYPE	157	120	86

Figure S440. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.0071

Table S441. Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 31(12P13.1) MUTATED	11	24	10	32
DEL PEAK 31(12P13.1) WILD-TYPE	68	151	69	75

Figure S441. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0496 (Fisher's exact test), Q value = 0.074

Table S442. Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 31(12P13.1) MUTATED	45	7	13
DEL PEAK 31(12P13.1) WILD-TYPE	156	66	59

Figure S442. Get High-res Image Gene #67: 'del_12p13.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q12' versus 'CN_CNMF'

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

Table S443. Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 32(12Q12) MUTATED	34	5	5	12	3
DEL PEAK 32(12Q12) WILD-TYPE	89	182	31	64	16

Figure S443. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q12' versus 'METHLYATION_CNMF'

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

Table S444. Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 32(12Q12) MUTATED	32	12	0	10
DEL PEAK 32(12Q12) WILD-TYPE	92	109	42	96

Figure S444. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.059

Table S445. Gene #68: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 32(12Q12) MUTATED	7	18	11	23
DEL PEAK 32(12Q12) WILD-TYPE	72	157	68	84

Figure S445. Get High-res Image Gene #68: 'del_12q12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

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

Table S446. Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 33(13Q12.11) MUTATED	25	9	3	23	3
DEL PEAK 33(13Q12.11) WILD-TYPE	98	178	33	53	16

Figure S446. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0475 (Fisher's exact test), Q value = 0.072

Table S447. Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 33(13Q12.11) MUTATED	25	18	2	11
DEL PEAK 33(13Q12.11) WILD-TYPE	99	103	40	95

Figure S447. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.036

Table S448. Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 33(13Q12.11) MUTATED	10	0	4	8	6	10	1
DEL PEAK 33(13Q12.11) WILD-TYPE	28	21	45	54	35	30	20

Figure S448. Get High-res Image Gene #69: 'del_13q12.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

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

Table S449. Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 34(14Q23.3) MUTATED	61	19	6	43	7
DEL PEAK 34(14Q23.3) WILD-TYPE	62	168	30	33	12

Figure S449. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

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

Table S450. Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 34(14Q23.3) MUTATED	70	29	6	18
DEL PEAK 34(14Q23.3) WILD-TYPE	54	92	36	88

Figure S450. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CNMF'

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

Table S451. Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 34(14Q23.3) MUTATED	11	14	13	6	33
DEL PEAK 34(14Q23.3) WILD-TYPE	54	48	33	31	29

Figure S451. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00071

Table S452. Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 34(14Q23.3) MUTATED	9	5	10	15	10	25	3
DEL PEAK 34(14Q23.3) WILD-TYPE	29	16	39	47	31	15	18

Figure S452. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CNMF'

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

Table S453. Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 34(14Q23.3) MUTATED	48	27	61
DEL PEAK 34(14Q23.3) WILD-TYPE	138	106	60

Figure S453. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S454. Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 34(14Q23.3) MUTATED	16	47	16	57
DEL PEAK 34(14Q23.3) WILD-TYPE	63	128	63	50

Figure S454. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.07

Table S455. Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 34(14Q23.3) MUTATED	34	18	13	16	12	13
DEL PEAK 34(14Q23.3) WILD-TYPE	42	40	47	42	24	45

Figure S455. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00269 (Fisher's exact test), Q value = 0.0055

Table S456. Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 34(14Q23.3) MUTATED	76	14	16
DEL PEAK 34(14Q23.3) WILD-TYPE	125	59	56

Figure S456. Get High-res Image Gene #70: 'del_14q23.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

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

Table S457. Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 35(14Q32.32) MUTATED	55	20	4	48	6
DEL PEAK 35(14Q32.32) WILD-TYPE	68	167	32	28	13

Figure S457. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

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

Table S458. Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 35(14Q32.32) MUTATED	62	28	8	21
DEL PEAK 35(14Q32.32) WILD-TYPE	62	93	34	85

Figure S458. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0038

Table S459. Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 35(14Q32.32) MUTATED	15	15	12	6	31
DEL PEAK 35(14Q32.32) WILD-TYPE	50	47	34	31	31

Figure S459. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S460. Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 35(14Q32.32) MUTATED	14	5	11	14	7	24	4
DEL PEAK 35(14Q32.32) WILD-TYPE	24	16	38	48	34	16	17

Figure S460. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00032

Table S461. Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 35(14Q32.32) MUTATED	49	29	55
DEL PEAK 35(14Q32.32) WILD-TYPE	137	104	66

Figure S461. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00703 (Fisher's exact test), Q value = 0.013

Table S462. Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 35(14Q32.32) MUTATED	18	51	18	46
DEL PEAK 35(14Q32.32) WILD-TYPE	61	124	61	61

Figure S462. Get High-res Image Gene #71: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

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

Table S463. Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 36(15Q11.2) MUTATED	61	16	10	27	6
DEL PEAK 36(15Q11.2) WILD-TYPE	62	171	26	49	13

Figure S463. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'METHLYATION_CNMF'

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

Table S464. Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 36(15Q11.2) MUTATED	56	30	4	20
DEL PEAK 36(15Q11.2) WILD-TYPE	68	91	38	86

Figure S464. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q11.2' versus 'RPPA_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.004

Table S465. Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 36(15Q11.2) MUTATED	21	11	31
DEL PEAK 36(15Q11.2) WILD-TYPE	61	79	60

Figure S465. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

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

Table S466. Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 36(15Q11.2) MUTATED	9	3	15	8	31
DEL PEAK 36(15Q11.2) WILD-TYPE	56	59	31	29	31

Figure S466. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S467. Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 36(15Q11.2) MUTATED	8	3	2	19	16	17	1
DEL PEAK 36(15Q11.2) WILD-TYPE	30	18	47	43	25	23	20

Figure S467. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00096

Table S468. Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 36(15Q11.2) MUTATED	49	23	48
DEL PEAK 36(15Q11.2) WILD-TYPE	137	110	73

Figure S468. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S469. Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 36(15Q11.2) MUTATED	18	44	11	47
DEL PEAK 36(15Q11.2) WILD-TYPE	61	131	68	60

Figure S469. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0287 (Fisher's exact test), Q value = 0.046

Table S470. Gene #72: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 36(15Q11.2) MUTATED	28	20	16	16	9	7
DEL PEAK 36(15Q11.2) WILD-TYPE	48	38	44	42	27	51

Figure S470. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00084

Table S471. Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 36(15Q11.2) MUTATED	69	8	19
DEL PEAK 36(15Q11.2) WILD-TYPE	132	65	53

Figure S471. Get High-res Image Gene #72: 'del_15q11.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

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

Table S472. Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 37(15Q15.1) MUTATED	63	15	9	29	6
DEL PEAK 37(15Q15.1) WILD-TYPE	60	172	27	47	13

Figure S472. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

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

Table S473. Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 37(15Q15.1) MUTATED	59	27	5	18
DEL PEAK 37(15Q15.1) WILD-TYPE	65	94	37	88

Figure S473. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.0075

Table S474. Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 37(15Q15.1) MUTATED	22	12	31
DEL PEAK 37(15Q15.1) WILD-TYPE	60	78	60

Figure S474. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_15q15.1' versus 'MRNASEQ_CNMF'

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

Table S475. Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 37(15Q15.1) MUTATED	11	3	16	7	31
DEL PEAK 37(15Q15.1) WILD-TYPE	54	59	30	30	31

Figure S475. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S476. Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 37(15Q15.1) MUTATED	10	4	1	19	14	19	1
DEL PEAK 37(15Q15.1) WILD-TYPE	28	17	48	43	27	21	20

Figure S476. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

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

Table S477. Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 37(15Q15.1) MUTATED	49	22	51
DEL PEAK 37(15Q15.1) WILD-TYPE	137	111	70

Figure S477. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S478. Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 37(15Q15.1) MUTATED	18	46	10	48
DEL PEAK 37(15Q15.1) WILD-TYPE	61	129	69	59

Figure S478. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00611 (Fisher's exact test), Q value = 0.011

Table S479. Gene #73: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 37(15Q15.1) MUTATED	31	16	16	16	9	6
DEL PEAK 37(15Q15.1) WILD-TYPE	45	42	44	42	27	52

Figure S479. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00052

Table S480. Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 37(15Q15.1) MUTATED	67	7	20
DEL PEAK 37(15Q15.1) WILD-TYPE	134	66	52

Figure S480. Get High-res Image Gene #73: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

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

Table S481. Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 38(16P13.3) MUTATED	54	10	3	24	2
DEL PEAK 38(16P13.3) WILD-TYPE	69	177	33	52	17

Figure S481. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

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

Table S482. Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 38(16P13.3) MUTATED	48	20	1	15
DEL PEAK 38(16P13.3) WILD-TYPE	76	101	41	91

Figure S482. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CNMF'

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

Table S483. Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 38(16P13.3) MUTATED	8	6	4	3	29
DEL PEAK 38(16P13.3) WILD-TYPE	57	56	42	34	33

Figure S483. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S484. Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 38(16P13.3) MUTATED	8	0	4	7	6	22	3
DEL PEAK 38(16P13.3) WILD-TYPE	30	21	45	55	35	18	18

Figure S484. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

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

Table S485. Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 38(16P13.3) MUTATED	26	14	53
DEL PEAK 38(16P13.3) WILD-TYPE	160	119	68

Figure S485. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S486. Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 38(16P13.3) MUTATED	7	30	9	47
DEL PEAK 38(16P13.3) WILD-TYPE	72	145	70	60

Figure S486. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S487. Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 38(16P13.3) MUTATED	34	10	5	7	13	5
DEL PEAK 38(16P13.3) WILD-TYPE	42	48	55	51	23	53

Figure S487. Get High-res Image Gene #74: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

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

Table S488. Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 39(16Q23.1) MUTATED	74	43	13	44	8
DEL PEAK 39(16Q23.1) WILD-TYPE	49	144	23	32	11

Figure S488. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00097

Table S489. Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 39(16Q23.1) MUTATED	66	53	13	29
DEL PEAK 39(16Q23.1) WILD-TYPE	58	68	29	77

Figure S489. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0037

Table S490. Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 39(16Q23.1) MUTATED	25	16	16	11	37
DEL PEAK 39(16Q23.1) WILD-TYPE	40	46	30	26	25

Figure S490. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00882 (Fisher's exact test), Q value = 0.016

Table S491. Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 39(16Q23.1) MUTATED	15	9	12	22	15	26	6
DEL PEAK 39(16Q23.1) WILD-TYPE	23	12	37	40	26	14	15

Figure S491. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S492. Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 39(16Q23.1) MUTATED	74	40	68
DEL PEAK 39(16Q23.1) WILD-TYPE	112	93	53

Figure S492. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00379 (Fisher's exact test), Q value = 0.0075

Table S493. Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 39(16Q23.1) MUTATED	31	71	22	58
DEL PEAK 39(16Q23.1) WILD-TYPE	48	104	57	49

Figure S493. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

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

Table S494. Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 39(16Q23.1) MUTATED	40	24	21	19	20	15
DEL PEAK 39(16Q23.1) WILD-TYPE	36	34	39	39	16	43

Figure S494. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0331 (Fisher's exact test), Q value = 0.052

Table S495. Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 39(16Q23.1) MUTATED	90	20	29
DEL PEAK 39(16Q23.1) WILD-TYPE	111	53	43

Figure S495. Get High-res Image Gene #75: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

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

Table S496. Gene #76: 'del_17p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 40(17P13.3) MUTATED	80	18	17	52	9
DEL PEAK 40(17P13.3) WILD-TYPE	43	169	19	24	10

Figure S496. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

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

Table S497. Gene #76: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 40(17P13.3) MUTATED	83	44	4	29
DEL PEAK 40(17P13.3) WILD-TYPE	41	77	38	77

Figure S497. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0201 (Fisher's exact test), Q value = 0.033

Table S498. Gene #76: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 40(17P13.3) MUTATED	12	41	13	32
DEL PEAK 40(17P13.3) WILD-TYPE	22	42	42	59

Figure S498. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p13.3' versus 'MRNASEQ_CNMF'

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

Table S499. Gene #76: 'del_17p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 40(17P13.3) MUTATED	14	13	18	13	38
DEL PEAK 40(17P13.3) WILD-TYPE	51	49	28	24	24

Figure S499. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S500. Gene #76: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 40(17P13.3) MUTATED	15	2	10	23	17	27	2
DEL PEAK 40(17P13.3) WILD-TYPE	23	19	39	39	24	13	19

Figure S500. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

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

Table S501. Gene #76: 'del_17p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 40(17P13.3) MUTATED	68	36	71
DEL PEAK 40(17P13.3) WILD-TYPE	118	97	50

Figure S501. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S502. Gene #76: 'del_17p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 40(17P13.3) MUTATED	26	68	20	61
DEL PEAK 40(17P13.3) WILD-TYPE	53	107	59	46

Figure S502. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0056

Table S503. Gene #76: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 40(17P13.3) MUTATED	96	19	25
DEL PEAK 40(17P13.3) WILD-TYPE	105	54	47

Figure S503. Get High-res Image Gene #76: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

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

Table S504. Gene #77: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 41(17P12) MUTATED	88	17	17	52	7
DEL PEAK 41(17P12) WILD-TYPE	35	170	19	24	12

Figure S504. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

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

Table S505. Gene #77: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 41(17P12) MUTATED	90	45	4	26
DEL PEAK 41(17P12) WILD-TYPE	34	76	38	80

Figure S505. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.014

Table S506. Gene #77: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 41(17P12) MUTATED	15	42	14	28
DEL PEAK 41(17P12) WILD-TYPE	19	41	41	63

Figure S506. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

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

Table S507. Gene #77: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 41(17P12) MUTATED	15	10	19	12	42
DEL PEAK 41(17P12) WILD-TYPE	50	52	27	25	20

Figure S507. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S508. Gene #77: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 41(17P12) MUTATED	14	2	7	25	17	30	3
DEL PEAK 41(17P12) WILD-TYPE	24	19	42	37	24	10	18

Figure S508. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

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

Table S509. Gene #77: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 41(17P12) MUTATED	72	31	77
DEL PEAK 41(17P12) WILD-TYPE	114	102	44

Figure S509. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S510. Gene #77: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 41(17P12) MUTATED	28	67	17	68
DEL PEAK 41(17P12) WILD-TYPE	51	108	62	39

Figure S510. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.026

Table S511. Gene #77: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 41(17P12) MUTATED	42	26	23	24	14	14
DEL PEAK 41(17P12) WILD-TYPE	34	32	37	34	22	44

Figure S511. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 4e-04

Table S512. Gene #77: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 41(17P12) MUTATED	97	15	31
DEL PEAK 41(17P12) WILD-TYPE	104	58	41

Figure S512. Get High-res Image Gene #77: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

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

Table S513. Gene #78: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 42(17Q24.3) MUTATED	35	10	6	19	6
DEL PEAK 42(17Q24.3) WILD-TYPE	88	177	30	57	13

Figure S513. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S514. Gene #78: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 42(17Q24.3) MUTATED	32	20	0	12
DEL PEAK 42(17Q24.3) WILD-TYPE	92	101	42	94

Figure S514. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17q24.3' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.03

Table S515. Gene #78: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 42(17Q24.3) MUTATED	7	5	6	10	16
DEL PEAK 42(17Q24.3) WILD-TYPE	58	57	40	27	46

Figure S515. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_17q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0051 (Fisher's exact test), Q value = 0.0097

Table S516. Gene #78: 'del_17q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 42(17Q24.3) MUTATED	6	0	4	7	12	12	3
DEL PEAK 42(17Q24.3) WILD-TYPE	32	21	45	55	29	28	18

Figure S516. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_17q24.3' versus 'MIRSEQ_CNMF'

P value = 0.00644 (Fisher's exact test), Q value = 0.012

Table S517. Gene #78: 'del_17q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 42(17Q24.3) MUTATED	27	16	32
DEL PEAK 42(17Q24.3) WILD-TYPE	159	117	89

Figure S517. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_17q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.063

Table S518. Gene #78: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 42(17Q24.3) MUTATED	13	23	11	28
DEL PEAK 42(17Q24.3) WILD-TYPE	66	152	68	79

Figure S518. Get High-res Image Gene #78: 'del_17q24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'CN_CNMF'

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

Table S519. Gene #79: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 43(18Q12.2) MUTATED	82	29	20	46	4
DEL PEAK 43(18Q12.2) WILD-TYPE	41	158	16	30	15

Figure S519. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

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

Table S520. Gene #79: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 43(18Q12.2) MUTATED	71	39	20	29
DEL PEAK 43(18Q12.2) WILD-TYPE	53	82	22	77

Figure S520. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MRNASEQ_CNMF'

P value = 0.00425 (Fisher's exact test), Q value = 0.0082

Table S521. Gene #79: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 43(18Q12.2) MUTATED	21	18	22	9	34
DEL PEAK 43(18Q12.2) WILD-TYPE	44	44	24	28	28

Figure S521. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00027

Table S522. Gene #79: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 43(18Q12.2) MUTATED	68	43	70
DEL PEAK 43(18Q12.2) WILD-TYPE	118	90	51

Figure S522. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.00091

Table S523. Gene #79: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 43(18Q12.2) MUTATED	25	69	25	62
DEL PEAK 43(18Q12.2) WILD-TYPE	54	106	54	45

Figure S523. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.002

Table S524. Gene #79: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 43(18Q12.2) MUTATED	44	17	19	27	16	15
DEL PEAK 43(18Q12.2) WILD-TYPE	32	41	41	31	20	43

Figure S524. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00724 (Fisher's exact test), Q value = 0.013

Table S525. Gene #79: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 43(18Q12.2) MUTATED	93	19	26
DEL PEAK 43(18Q12.2) WILD-TYPE	108	54	46

Figure S525. Get High-res Image Gene #79: 'del_18q12.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

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

Table S526. Gene #80: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 44(18Q21.2) MUTATED	89	35	25	51	4
DEL PEAK 44(18Q21.2) WILD-TYPE	34	152	11	25	15

Figure S526. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

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

Table S527. Gene #80: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 44(18Q21.2) MUTATED	79	49	21	33
DEL PEAK 44(18Q21.2) WILD-TYPE	45	72	21	73

Figure S527. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00077

Table S528. Gene #80: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 44(18Q21.2) MUTATED	26	19	23	11	41
DEL PEAK 44(18Q21.2) WILD-TYPE	39	43	23	26	21

Figure S528. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00423 (Fisher's exact test), Q value = 0.0082

Table S529. Gene #80: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 44(18Q21.2) MUTATED	17	13	15	28	20	24	3
DEL PEAK 44(18Q21.2) WILD-TYPE	21	8	34	34	21	16	18

Figure S529. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

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

Table S530. Gene #80: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 44(18Q21.2) MUTATED	80	48	76
DEL PEAK 44(18Q21.2) WILD-TYPE	106	85	45

Figure S530. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0041

Table S531. Gene #80: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 44(18Q21.2) MUTATED	33	77	28	66
DEL PEAK 44(18Q21.2) WILD-TYPE	46	98	51	41

Figure S531. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0029

Table S532. Gene #80: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 44(18Q21.2) MUTATED	48	19	23	31	16	19
DEL PEAK 44(18Q21.2) WILD-TYPE	28	39	37	27	20	39

Figure S532. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00942 (Fisher's exact test), Q value = 0.017

Table S533. Gene #80: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 44(18Q21.2) MUTATED	102	22	32
DEL PEAK 44(18Q21.2) WILD-TYPE	99	51	40

Figure S533. Get High-res Image Gene #80: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

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

Table S534. Gene #81: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 45(19P13.3) MUTATED	92	9	12	42	7
DEL PEAK 45(19P13.3) WILD-TYPE	31	178	24	34	12

Figure S534. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

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

Table S535. Gene #81: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 45(19P13.3) MUTATED	92	30	5	19
DEL PEAK 45(19P13.3) WILD-TYPE	32	91	37	87

Figure S535. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 0.00422 (Fisher's exact test), Q value = 0.0082

Table S536. Gene #81: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 45(19P13.3) MUTATED	24	21	42
DEL PEAK 45(19P13.3) WILD-TYPE	58	69	49

Figure S536. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00448 (Fisher's exact test), Q value = 0.0086

Table S537. Gene #81: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 45(19P13.3) MUTATED	11	40	13	23
DEL PEAK 45(19P13.3) WILD-TYPE	23	43	42	68

Figure S537. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

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

Table S538. Gene #81: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 45(19P13.3) MUTATED	13	4	13	8	47
DEL PEAK 45(19P13.3) WILD-TYPE	52	58	33	29	15

Figure S538. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S539. Gene #81: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 45(19P13.3) MUTATED	14	2	4	21	12	30	2
DEL PEAK 45(19P13.3) WILD-TYPE	24	19	45	41	29	10	19

Figure S539. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

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

Table S540. Gene #81: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 45(19P13.3) MUTATED	53	23	85
DEL PEAK 45(19P13.3) WILD-TYPE	133	110	36

Figure S540. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S541. Gene #81: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 45(19P13.3) MUTATED	20	49	7	85
DEL PEAK 45(19P13.3) WILD-TYPE	59	126	72	22

Figure S541. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

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

Table S542. Gene #81: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 45(19P13.3) MUTATED	50	17	17	20	18	7
DEL PEAK 45(19P13.3) WILD-TYPE	26	41	43	38	18	51

Figure S542. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S543. Gene #81: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 45(19P13.3) MUTATED	91	10	28
DEL PEAK 45(19P13.3) WILD-TYPE	110	63	44

Figure S543. Get High-res Image Gene #81: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

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

Table S544. Gene #82: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 46(19Q13.11) MUTATED	41	5	6	16	7
DEL PEAK 46(19Q13.11) WILD-TYPE	82	182	30	60	12

Figure S544. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.11' versus 'METHLYATION_CNMF'

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

Table S545. Gene #82: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 46(19Q13.11) MUTATED	47	16	1	4
DEL PEAK 46(19Q13.11) WILD-TYPE	77	105	41	102

Figure S545. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

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

Table S546. Gene #82: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 46(19Q13.11) MUTATED	6	2	6	3	21
DEL PEAK 46(19Q13.11) WILD-TYPE	59	60	40	34	41

Figure S546. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0016

Table S547. Gene #82: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 46(19Q13.11) MUTATED	2	1	2	11	7	14	1
DEL PEAK 46(19Q13.11) WILD-TYPE	36	20	47	51	34	26	20

Figure S547. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_CNMF'

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

Table S548. Gene #82: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 46(19Q13.11) MUTATED	26	8	41
DEL PEAK 46(19Q13.11) WILD-TYPE	160	125	80

Figure S548. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S549. Gene #82: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 46(19Q13.11) MUTATED	12	16	5	42
DEL PEAK 46(19Q13.11) WILD-TYPE	67	159	74	65

Figure S549. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00572 (Fisher's exact test), Q value = 0.011

Table S550. Gene #82: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 46(19Q13.11) MUTATED	24	11	10	6	6	4
DEL PEAK 46(19Q13.11) WILD-TYPE	52	47	50	52	30	54

Figure S550. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00895 (Fisher's exact test), Q value = 0.016

Table S551. Gene #82: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 46(19Q13.11) MUTATED	38	5	18
DEL PEAK 46(19Q13.11) WILD-TYPE	163	68	54

Figure S551. Get High-res Image Gene #82: 'del_19q13.11' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0025

Table S552. Gene #83: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 47(20P12.1) MUTATED	20	8	1	10	0
DEL PEAK 47(20P12.1) WILD-TYPE	103	179	35	66	19

Figure S552. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00059

Table S553. Gene #83: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 47(20P12.1) MUTATED	24	7	1	5
DEL PEAK 47(20P12.1) WILD-TYPE	100	114	41	101

Figure S553. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.026

Table S554. Gene #83: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 47(20P12.1) MUTATED	3	2	9	1	7
DEL PEAK 47(20P12.1) WILD-TYPE	62	60	37	36	55

Figure S554. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0028

Table S555. Gene #83: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 47(20P12.1) MUTATED	11	7	21
DEL PEAK 47(20P12.1) WILD-TYPE	175	126	100

Figure S555. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.04 (Fisher's exact test), Q value = 0.062

Table S556. Gene #83: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 47(20P12.1) MUTATED	21	2	10
DEL PEAK 47(20P12.1) WILD-TYPE	180	71	62

Figure S556. Get High-res Image Gene #83: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

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

Table S557. Gene #84: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 48(21Q11.2) MUTATED	75	35	16	46	11
DEL PEAK 48(21Q11.2) WILD-TYPE	48	152	20	30	8

Figure S557. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

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

Table S558. Gene #84: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 48(21Q11.2) MUTATED	74	48	7	39
DEL PEAK 48(21Q11.2) WILD-TYPE	50	73	35	67

Figure S558. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00286 (Fisher's exact test), Q value = 0.0058

Table S559. Gene #84: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 48(21Q11.2) MUTATED	18	17	13	11	35
DEL PEAK 48(21Q11.2) WILD-TYPE	47	45	33	26	27

Figure S559. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0044

Table S560. Gene #84: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 48(21Q11.2) MUTATED	18	2	14	18	16	22	4
DEL PEAK 48(21Q11.2) WILD-TYPE	20	19	35	44	25	18	17

Figure S560. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

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

Table S561. Gene #84: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 48(21Q11.2) MUTATED	68	43	72
DEL PEAK 48(21Q11.2) WILD-TYPE	118	90	49

Figure S561. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0017

Table S562. Gene #84: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 48(21Q11.2) MUTATED	25	68	28	62
DEL PEAK 48(21Q11.2) WILD-TYPE	54	107	51	45

Figure S562. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0035

Table S563. Gene #84: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 48(21Q11.2) MUTATED	42	26	17	24	22	17
DEL PEAK 48(21Q11.2) WILD-TYPE	34	32	43	34	14	41

Figure S563. Get High-res Image Gene #84: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_21q22.3' versus 'CN_CNMF'

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

Table S564. Gene #85: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 49(21Q22.3) MUTATED	73	39	17	53	11
DEL PEAK 49(21Q22.3) WILD-TYPE	50	148	19	23	8

Figure S564. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

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

Table S565. Gene #85: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 49(21Q22.3) MUTATED	71	55	6	42
DEL PEAK 49(21Q22.3) WILD-TYPE	53	66	36	64

Figure S565. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MRNASEQ_CNMF'

P value = 0.0055 (Fisher's exact test), Q value = 0.01

Table S566. Gene #85: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 49(21Q22.3) MUTATED	19	17	17	11	35
DEL PEAK 49(21Q22.3) WILD-TYPE	46	45	29	26	27

Figure S566. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_21q22.3' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S567. Gene #85: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 49(21Q22.3) MUTATED	19	2	14	21	17	23	3
DEL PEAK 49(21Q22.3) WILD-TYPE	19	19	35	41	24	17	18

Figure S567. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S568. Gene #85: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 49(21Q22.3) MUTATED	78	44	71
DEL PEAK 49(21Q22.3) WILD-TYPE	108	89	50

Figure S568. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.006

Table S569. Gene #85: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 49(21Q22.3) MUTATED	29	76	26	62
DEL PEAK 49(21Q22.3) WILD-TYPE	50	99	53	45

Figure S569. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00069

Table S570. Gene #85: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 49(21Q22.3) MUTATED	42	32	21	21	24	16
DEL PEAK 49(21Q22.3) WILD-TYPE	34	26	39	37	12	42

Figure S570. Get High-res Image Gene #85: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'CN_CNMF'

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

Table S571. Gene #86: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 50(22Q13.31) MUTATED	73	21	11	47	9
DEL PEAK 50(22Q13.31) WILD-TYPE	50	166	25	29	10

Figure S571. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

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

Table S572. Gene #86: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 50(22Q13.31) MUTATED	75	40	4	25
DEL PEAK 50(22Q13.31) WILD-TYPE	49	81	38	81

Figure S572. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'RPPA_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.074

Table S573. Gene #86: 'del_22q13.31' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	82	90	91
DEL PEAK 50(22Q13.31) MUTATED	21	28	39
DEL PEAK 50(22Q13.31) WILD-TYPE	61	62	52

Figure S573. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #3: 'RPPA_CNMF'

'del_22q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00602 (Fisher's exact test), Q value = 0.011

Table S574. Gene #86: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 50(22Q13.31) MUTATED	9	40	12	27
DEL PEAK 50(22Q13.31) WILD-TYPE	25	43	43	64

Figure S574. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_22q13.31' versus 'MRNASEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.003

Table S575. Gene #86: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 50(22Q13.31) MUTATED	14	15	18	11	33
DEL PEAK 50(22Q13.31) WILD-TYPE	51	47	28	26	29

Figure S575. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 0.0082

Table S576. Gene #86: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 50(22Q13.31) MUTATED	15	3	10	24	15	21	3
DEL PEAK 50(22Q13.31) WILD-TYPE	23	18	39	38	26	19	18

Figure S576. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

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

Table S577. Gene #86: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 50(22Q13.31) MUTATED	56	34	70
DEL PEAK 50(22Q13.31) WILD-TYPE	130	99	51

Figure S577. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S578. Gene #86: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 50(22Q13.31) MUTATED	24	54	18	64
DEL PEAK 50(22Q13.31) WILD-TYPE	55	121	61	43

Figure S578. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00045

Table S579. Gene #86: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	76	58	60	58	36	58
DEL PEAK 50(22Q13.31) MUTATED	41	22	22	12	19	13
DEL PEAK 50(22Q13.31) WILD-TYPE	35	36	38	46	17	45

Figure S579. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.024

Table S580. Gene #86: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	201	73	72
DEL PEAK 50(22Q13.31) MUTATED	85	17	27
DEL PEAK 50(22Q13.31) WILD-TYPE	116	56	45

Figure S580. Get High-res Image Gene #86: 'del_22q13.31' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

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

Table S581. Gene #87: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 51(XP22.2) MUTATED	42	11	4	24	4
DEL PEAK 51(XP22.2) WILD-TYPE	81	176	32	52	15

Figure S581. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00057

Table S582. Gene #87: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 51(XP22.2) MUTATED	39	24	2	14
DEL PEAK 51(XP22.2) WILD-TYPE	85	97	40	92

Figure S582. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.065

Table S583. Gene #87: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 51(XP22.2) MUTATED	9	23	6	14
DEL PEAK 51(XP22.2) WILD-TYPE	25	60	49	77

Figure S583. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00034

Table S584. Gene #87: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 51(XP22.2) MUTATED	3	8	9	10	21
DEL PEAK 51(XP22.2) WILD-TYPE	62	54	37	27	41

Figure S584. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00077

Table S585. Gene #87: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	38	21	49	62	41	40	21
DEL PEAK 51(XP22.2) MUTATED	11	0	5	11	15	9	0
DEL PEAK 51(XP22.2) WILD-TYPE	27	21	44	51	26	31	21

Figure S585. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.0058

Table S586. Gene #87: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	79	175	79	107
DEL PEAK 51(XP22.2) MUTATED	13	29	9	34
DEL PEAK 51(XP22.2) WILD-TYPE	66	146	70	73

Figure S586. Get High-res Image Gene #87: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

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

Table S587. Gene #88: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 52(XP21.1) MUTATED	35	8	7	21	3
DEL PEAK 52(XP21.1) WILD-TYPE	88	179	29	55	16

Figure S587. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.0068

Table S588. Gene #88: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 52(XP21.1) MUTATED	29	23	1	13
DEL PEAK 52(XP21.1) WILD-TYPE	95	98	41	93

Figure S588. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0313 (Fisher's exact test), Q value = 0.05

Table S589. Gene #88: 'del_xp21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 52(XP21.1) MUTATED	5	21	4	12
DEL PEAK 52(XP21.1) WILD-TYPE	29	62	51	79

Figure S589. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 0.00861 (Fisher's exact test), Q value = 0.016

Table S590. Gene #88: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 52(XP21.1) MUTATED	2	8	9	7	14
DEL PEAK 52(XP21.1) WILD-TYPE	63	54	37	30	48

Figure S590. Get High-res Image Gene #88: 'del_xp21.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'CN_CNMF'

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

Table S591. Gene #89: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	123	187	36	76	19
DEL PEAK 53(XQ21.33) MUTATED	27	6	5	17	1
DEL PEAK 53(XQ21.33) WILD-TYPE	96	181	31	59	18

Figure S591. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.0042 (Fisher's exact test), Q value = 0.0082

Table S592. Gene #89: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	124	121	42	106
DEL PEAK 53(XQ21.33) MUTATED	25	15	2	6
DEL PEAK 53(XQ21.33) WILD-TYPE	99	106	40	100

Figure S592. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.055

Table S593. Gene #89: 'del_xq21.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	34	83	55	91
DEL PEAK 53(XQ21.33) MUTATED	5	19	6	7
DEL PEAK 53(XQ21.33) WILD-TYPE	29	64	49	84

Figure S593. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.00806 (Fisher's exact test), Q value = 0.015

Table S594. Gene #89: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	65	62	46	37	62
DEL PEAK 53(XQ21.33) MUTATED	3	4	7	5	15
DEL PEAK 53(XQ21.33) WILD-TYPE	62	58	39	32	47

Figure S594. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.023

Table S595. Gene #89: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	186	133	121
DEL PEAK 53(XQ21.33) MUTATED	22	10	24
DEL PEAK 53(XQ21.33) WILD-TYPE	164	123	97

Figure S595. Get High-res Image Gene #89: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/STAD-TP/15098840/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/15114286/STAD-TP.transferedmergedcluster.txt
Number of patients = 441
Number of significantly focal cnvs = 89
Number of molecular subtypes = 10
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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