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

Stomach and Esophageal carcinoma (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/C1PG1QTX

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 99 focal events and 8 molecular subtypes across 625 patients, 649 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p36.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p34.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_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 'MIRSEQ_CNMF'.
amp_9p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_10p11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_10q26.13 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.43 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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_CNMF'.
del_1q44 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_1q44 cnv correlated to 'METHLYATION_CNMF'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q32.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q33.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p26.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_3q26.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
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_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q16.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q21.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q23.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q32.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_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_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q24.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_18q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', and 'MIRSEQ_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q22.13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q11.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_xq21.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 99 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 649 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
amp 1q21 3	249 (40%)	376	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.0087 (0.012)	1e-05 (2.39e-05)	3e-05 (6.66e-05)	1e-05 (2.39e-05)	4e-05 (8.56e-05)	1e-05 (2.39e-05)
amp 1q42 3	244 (39%)	381	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00799 (0.0112)	5e-05 (0.000105)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	2e-05 (4.59e-05)
amp 2q12 2	155 (25%)	470	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00046 (0.000813)	0.00012 (0.000234)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	6e-05 (0.000124)	0.0001 (0.000198)
amp 3q26 2	287 (46%)	338	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
amp 5p15 33	228 (36%)	397	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
amp 5p13 1	216 (35%)	409	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
amp 6p21 1	192 (31%)	433	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.03 (0.0381)	1e-05 (2.39e-05)	5e-05 (0.000105)	1e-05 (2.39e-05)	0.00199 (0.00316)	1e-05 (2.39e-05)
amp 7p22 3	353 (56%)	272	1e-05 (2.39e-05)	1e-05 (2.39e-05)	7e-05 (0.000143)	6e-05 (0.000124)	2e-05 (4.59e-05)	1e-05 (2.39e-05)	2e-05 (4.59e-05)	1e-05 (2.39e-05)
amp 7p11 2	340 (54%)	285	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00014 (0.000266)	0.00033 (0.000593)	7e-05 (0.000143)	0.00419 (0.00617)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
amp 7q21 2	317 (51%)	308	1e-05 (2.39e-05)	0.00018 (0.000338)	0.00021 (0.00039)	0.0387 (0.048)	0.00324 (0.00487)	0.00242 (0.00373)	1e-05 (2.39e-05)	0.00399 (0.00591)
amp 8p23 1	229 (37%)	396	3e-05 (6.66e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	4e-05 (8.56e-05)	8e-05 (0.000161)	0.00014 (0.000266)	0.00014 (0.000266)
amp 8q24 21	454 (73%)	171	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00036 (0.000641)	2e-05 (4.59e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00018 (0.000338)	2e-05 (4.59e-05)
amp 11q13 3	218 (35%)	407	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
amp 12p12 1	207 (33%)	418	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00134 (0.00222)	0.00064 (0.0011)	4e-05 (8.56e-05)	7e-05 (0.000143)	0.00025 (0.000458)	0.00209 (0.00329)
amp 14q13 3	113 (18%)	512	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	6e-05 (0.000124)	1e-05 (2.39e-05)
amp 18p11 32	178 (28%)	447	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00077 (0.00131)	4e-05 (8.56e-05)	3e-05 (6.66e-05)	1e-05 (2.39e-05)	0.00067 (0.00115)	0.00047 (0.000829)
amp xq28	154 (25%)	471	1e-05 (2.39e-05)	2e-05 (4.59e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.003 (0.00454)	1e-05 (2.39e-05)
del 1p36 11	210 (34%)	415	1e-05 (2.39e-05)	0.00031 (0.000559)	1e-05 (2.39e-05)	0.00064 (0.0011)	0.0002 (0.000373)	6e-05 (0.000124)	0.00243 (0.00374)	0.00063 (0.00109)
del 2q22 1	126 (20%)	499	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 2q33 3	85 (14%)	540	1e-05 (2.39e-05)	6e-05 (0.000124)	0.00031 (0.000559)	0.0011 (0.00185)	0.00014 (0.000266)	0.00056 (0.000973)	0.00198 (0.00316)	0.00193 (0.00308)
del 2q37 2	122 (20%)	503	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00019 (0.000355)	3e-05 (6.66e-05)	0.00018 (0.000338)	1e-05 (2.39e-05)	0.0204 (0.0266)	4e-05 (8.56e-05)
del 3p26 2	250 (40%)	375	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 3p14 2	282 (45%)	343	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 4p16 3	271 (43%)	354	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00504 (0.00727)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 4p15 2	269 (43%)	356	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00207 (0.00327)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 4q22 1	298 (48%)	327	1e-05 (2.39e-05)	0.00362 (0.00539)	0.00761 (0.0107)	6e-05 (0.000124)	0.0029 (0.00441)	0.00097 (0.00165)	0.0121 (0.0164)	0.0284 (0.0361)
del 5q12 1	282 (45%)	343	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 6p25 3	188 (30%)	437	1e-05 (2.39e-05)	7e-05 (0.000143)	0.00125 (0.00208)	0.00023 (0.000423)	0.00018 (0.000338)	8e-05 (0.000161)	0.0385 (0.0479)	0.00031 (0.000559)
del 7q36 3	163 (26%)	462	1e-05 (2.39e-05)	8e-05 (0.000161)	0.00185 (0.00297)	0.00013 (0.000251)	2e-05 (4.59e-05)	1e-05 (2.39e-05)	0.00034 (0.000609)	0.0126 (0.0169)
del 8p23 2	212 (34%)	413	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 9p23	302 (48%)	323	1e-05 (2.39e-05)	0.00133 (0.0022)	0.0156 (0.0207)	0.00509 (0.00733)	0.00108 (0.00182)	4e-05 (8.56e-05)	0.043 (0.0527)	0.0311 (0.0394)
del 9p21 3	334 (53%)	291	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 9q21 11	176 (28%)	449	1e-05 (2.39e-05)	9e-05 (0.000179)	0.0209 (0.0272)	0.00016 (0.000303)	0.00013 (0.000251)	1e-05 (2.39e-05)	0.00105 (0.00178)	0.00568 (0.00815)
del 10p15 3	131 (21%)	494	1e-05 (2.39e-05)	0.00209 (0.00329)	4e-05 (8.56e-05)	0.0001 (0.000198)	0.00235 (0.00365)	8e-05 (0.000161)	0.0069 (0.00976)	3e-05 (6.66e-05)
del 10p11 21	102 (16%)	523	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	4e-05 (8.56e-05)	1e-05 (2.39e-05)
del 10q21 1	112 (18%)	513	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00222 (0.00347)	3e-05 (6.66e-05)	0.00114 (0.00191)	1e-05 (2.39e-05)	0.00652 (0.00929)	3e-05 (6.66e-05)
del 10q22 3	135 (22%)	490	1e-05 (2.39e-05)	1e-05 (2.39e-05)	5e-05 (0.000105)	1e-05 (2.39e-05)	3e-05 (6.66e-05)	1e-05 (2.39e-05)	0.00013 (0.000251)	1e-05 (2.39e-05)
del 10q23 31	183 (29%)	442	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00014 (0.000266)	1e-05 (2.39e-05)	3e-05 (6.66e-05)	1e-05 (2.39e-05)	0.0005 (0.000878)	5e-05 (0.000105)
del 11p15 5	175 (28%)	450	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	8e-05 (0.000161)	2e-05 (4.59e-05)	0.00026 (0.000473)	0.00054 (0.000944)
del 11q25	178 (28%)	447	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 13q12 11	138 (22%)	487	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 13q14 2	125 (20%)	500	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 13q21 31	126 (20%)	499	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	2e-05 (4.59e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	2e-05 (4.59e-05)	1e-05 (2.39e-05)
del 19p13 3	249 (40%)	376	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)
del 19q13 11	120 (19%)	505	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00147 (0.00241)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	9e-05 (0.000179)	0.00032 (0.000576)
del 21q11 2	290 (46%)	335	1e-05 (2.39e-05)	0.0107 (0.0145)	0.00019 (0.000355)	1e-05 (2.39e-05)	0.00023 (0.000423)	1e-05 (2.39e-05)	0.00403 (0.00595)	0.00159 (0.0026)
del 21q22 13	305 (49%)	320	1e-05 (2.39e-05)	0.0214 (0.0279)	0.00067 (0.00115)	5e-05 (0.000105)	0.00138 (0.00227)	0.00108 (0.00182)	0.00366 (0.00544)	0.0124 (0.0167)
del xp21 1	143 (23%)	482	1e-05 (2.39e-05)	2e-05 (4.59e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	3e-05 (6.66e-05)	0.00694 (0.0098)	5e-05 (0.000105)
del xp11 3	146 (23%)	479	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00469 (0.00683)	1e-05 (2.39e-05)
amp 6q12	141 (23%)	484	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.149 (0.163)	1e-05 (2.39e-05)	0.00409 (0.00603)	1e-05 (2.39e-05)	0.00113 (0.0019)	2e-05 (4.59e-05)
amp 15q26 1	168 (27%)	457	1e-05 (2.39e-05)	0.0656 (0.0783)	0.00049 (0.000862)	1e-05 (2.39e-05)	0.00081 (0.00138)	0.00026 (0.000473)	0.0496 (0.0605)	0.00031 (0.000559)
amp 17q12	222 (36%)	403	1e-05 (2.39e-05)	0.00022 (0.000408)	0.00646 (0.00922)	0.00477 (0.00693)	0.0312 (0.0394)	0.00055 (0.000957)	0.0661 (0.0786)	0.00014 (0.000266)
del 1p13 2	156 (25%)	469	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.00023 (0.000423)	0.00023 (0.000423)	0.0107 (0.0145)	0.00163 (0.00266)	0.00546 (0.00785)	0.0559 (0.0673)
del 6q26	152 (24%)	473	1e-05 (2.39e-05)	0.0713 (0.0837)	0.0236 (0.0304)	0.0486 (0.0594)	0.0111 (0.015)	0.041 (0.0506)	0.0268 (0.0343)	0.0379 (0.0473)
del 7q31 1	127 (20%)	498	1e-05 (2.39e-05)	0.00479 (0.00695)	0.00378 (0.00561)	0.00763 (0.0107)	0.0077 (0.0108)	0.00672 (0.00956)	0.153 (0.167)	0.0166 (0.0219)
del 16p13 3	178 (28%)	447	1e-05 (2.39e-05)	0.00438 (0.00642)	0.0535 (0.0647)	1e-05 (2.39e-05)	0.00242 (0.00373)	1e-05 (2.39e-05)	0.00236 (0.00366)	1e-05 (2.39e-05)
del 16p13 3	148 (24%)	477	1e-05 (2.39e-05)	0.0133 (0.0178)	0.297 (0.312)	1e-05 (2.39e-05)	0.00035 (0.000624)	1e-05 (2.39e-05)	0.00234 (0.00364)	1e-05 (2.39e-05)
del 16q23 1	265 (42%)	360	1e-05 (2.39e-05)	0.00068 (0.00117)	0.133 (0.147)	1e-05 (2.39e-05)	0.00323 (0.00486)	1e-05 (2.39e-05)	0.00938 (0.0129)	1e-05 (2.39e-05)
del 17p12	267 (43%)	358	1e-05 (2.39e-05)	7e-05 (0.000143)	0.00204 (0.00323)	1e-05 (2.39e-05)	0.00055 (0.000957)	1e-05 (2.39e-05)	0.063 (0.0754)	1e-05 (2.39e-05)
del 22q13 31	235 (38%)	390	1e-05 (2.39e-05)	0.00269 (0.00411)	0.15 (0.164)	1e-05 (2.39e-05)	0.00011 (0.000216)	1e-05 (2.39e-05)	0.0288 (0.0367)	3e-05 (6.66e-05)
del xp22 2	150 (24%)	475	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.0004 (0.00071)	4e-05 (8.56e-05)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.0626 (0.0751)	0.00138 (0.00227)
del xq21 33	96 (15%)	529	1e-05 (2.39e-05)	0.00756 (0.0107)	0.00797 (0.0112)	0.00998 (0.0136)	0.0103 (0.0141)	0.0383 (0.0478)	0.0417 (0.0513)	0.186 (0.2)
amp 1p36 22	101 (16%)	524	1e-05 (2.39e-05)	0.00622 (0.00889)	0.148 (0.162)	0.0082 (0.0114)	0.0384 (0.0478)	0.00126 (0.0021)	0.19 (0.204)	0.00117 (0.00195)
amp 13q12 3	216 (35%)	409	1e-05 (2.39e-05)	0.0859 (0.0981)	1e-05 (2.39e-05)	1e-05 (2.39e-05)	0.0105 (0.0143)	1e-05 (2.39e-05)	0.646 (0.654)	1e-05 (2.39e-05)
amp 13q22 1	243 (39%)	382	1e-05 (2.39e-05)	0.00223 (0.00348)	0.00011 (0.000216)	1e-05 (2.39e-05)	0.0945 (0.107)	1e-05 (2.39e-05)	0.126 (0.14)	1e-05 (2.39e-05)
amp 19q12	185 (30%)	440	1e-05 (2.39e-05)	9e-05 (0.000179)	0.126 (0.141)	1e-05 (2.39e-05)	0.0153 (0.0204)	1e-05 (2.39e-05)	0.101 (0.115)	1e-05 (2.39e-05)
del 4q34 3	300 (48%)	325	1e-05 (2.39e-05)	0.00191 (0.00306)	0.5 (0.512)	4e-05 (8.56e-05)	0.0199 (0.0261)	1e-05 (2.39e-05)	0.127 (0.141)	1e-05 (2.39e-05)
del 18q21 2	323 (52%)	302	1e-05 (2.39e-05)	0.00046 (0.000813)	0.0614 (0.0737)	0.0414 (0.0511)	0.0136 (0.0182)	0.00443 (0.00649)	0.127 (0.141)	0.0403 (0.0499)
del 22q11 1	230 (37%)	395	1e-05 (2.39e-05)	0.00596 (0.00854)	0.118 (0.133)	1e-05 (2.39e-05)	0.00185 (0.00297)	1e-05 (2.39e-05)	0.0759 (0.0883)	4e-05 (8.56e-05)
amp 1p34 2	95 (15%)	530	1e-05 (2.39e-05)	0.00488 (0.00705)	0.0866 (0.0988)	0.0181 (0.0239)	0.0333 (0.0419)	0.067 (0.0796)	0.0705 (0.0831)	0.00292 (0.00443)
amp 6q21	111 (18%)	514	1e-05 (2.39e-05)	0.00214 (0.00336)	0.702 (0.707)	5e-05 (0.000105)	0.161 (0.175)	1e-05 (2.39e-05)	0.173 (0.187)	1e-05 (2.39e-05)
amp 9q34 3	185 (30%)	440	1e-05 (2.39e-05)	0.00436 (0.00641)	0.00237 (0.00367)	0.0521 (0.0633)	0.0109 (0.0148)	0.218 (0.233)	0.0185 (0.0243)	0.0735 (0.0861)
amp 10p11 22	169 (27%)	456	1e-05 (2.39e-05)	0.00203 (0.00322)	0.291 (0.307)	0.00481 (0.00696)	0.607 (0.616)	0.00012 (0.000234)	0.124 (0.139)	0.0207 (0.0271)
amp 10q26 13	119 (19%)	506	4e-05 (8.56e-05)	0.79 (0.794)	0.353 (0.369)	0.00011 (0.000216)	0.0141 (0.0189)	0.00329 (0.00493)	0.13 (0.144)	0.00248 (0.00381)
amp 18q11 2	198 (32%)	427	1e-05 (2.39e-05)	0.0837 (0.0961)	0.0443 (0.0543)	0.00072 (0.00123)	0.114 (0.128)	0.00026 (0.000473)	0.0537 (0.0649)	0.00974 (0.0133)
amp 19q13 43	164 (26%)	461	1e-05 (2.39e-05)	0.0424 (0.0521)	0.509 (0.52)	0.417 (0.43)	0.343 (0.359)	0.0025 (0.00383)	0.00302 (0.00456)	0.00179 (0.00289)
amp 20q13 2	416 (67%)	209	1e-05 (2.39e-05)	0.071 (0.0835)	0.00175 (0.00283)	1e-05 (2.39e-05)	0.0704 (0.0831)	1e-05 (2.39e-05)	0.234 (0.249)	1e-05 (2.39e-05)
del 3q26 31	63 (10%)	562	1e-05 (2.39e-05)	0.0082 (0.0114)	0.0893 (0.102)	2e-05 (4.59e-05)	0.216 (0.231)	9e-05 (0.000179)	0.107 (0.12)	2e-05 (4.59e-05)
del 6q16 3	147 (24%)	478	1e-05 (2.39e-05)	0.0263 (0.0336)	0.00873 (0.012)	0.00865 (0.012)	0.151 (0.164)	0.00829 (0.0115)	0.0892 (0.102)	0.0743 (0.0869)
del 12p13 1	113 (18%)	512	1e-05 (2.39e-05)	0.0423 (0.052)	0.57 (0.581)	1e-05 (2.39e-05)	0.617 (0.624)	1e-05 (2.39e-05)	0.408 (0.421)	0.00014 (0.000266)
del 12q23 1	109 (17%)	516	1e-05 (2.39e-05)	0.00281 (0.00428)	0.0162 (0.0214)	0.00013 (0.000251)	0.148 (0.162)	0.00935 (0.0129)	0.238 (0.252)	0.19 (0.204)
del 14q23 3	187 (30%)	438	1e-05 (2.39e-05)	0.00272 (0.00415)	0.225 (0.24)	1e-05 (2.39e-05)	0.201 (0.216)	1e-05 (2.39e-05)	0.174 (0.188)	8e-05 (0.000161)
del 14q32 32	190 (30%)	435	1e-05 (2.39e-05)	0.023 (0.0298)	0.315 (0.331)	0.00168 (0.00273)	0.419 (0.432)	0.00215 (0.00337)	0.546 (0.557)	0.0134 (0.018)
del 15q11 2	183 (29%)	442	1e-05 (2.39e-05)	0.0843 (0.0965)	0.00182 (0.00294)	0.00128 (0.00213)	0.0231 (0.0298)	1e-05 (2.39e-05)	0.0749 (0.0873)	0.0833 (0.0959)
del 18q12 2	292 (47%)	333	1e-05 (2.39e-05)	0.00165 (0.00268)	0.0753 (0.0877)	0.0807 (0.0936)	0.0327 (0.0413)	0.00234 (0.00364)	0.0993 (0.113)	0.0257 (0.033)
del xq11 2	103 (16%)	522	1e-05 (2.39e-05)	0.0181 (0.0239)	0.00054 (0.000944)	0.00453 (0.00661)	0.00447 (0.00653)	0.145 (0.16)	0.0695 (0.0822)	0.0829 (0.0956)
amp 9p13 3	132 (21%)	493	0.00035 (0.000624)	0.398 (0.413)	0.00332 (0.00497)	0.164 (0.177)	0.0258 (0.0331)	0.109 (0.123)	0.066 (0.0786)	0.0068 (0.00963)
amp 11p13	138 (22%)	487	1e-05 (2.39e-05)	0.00165 (0.00268)	0.126 (0.141)	0.00809 (0.0113)	0.137 (0.151)	0.00187 (0.003)	0.0745 (0.0871)	0.0504 (0.0614)
amp 19p13 2	79 (13%)	546	1e-05 (2.39e-05)	0.00146 (0.0024)	0.0688 (0.0814)	0.22 (0.235)	0.371 (0.387)	0.113 (0.128)	0.039 (0.0484)	0.0364 (0.0457)
del 1q44	46 (7%)	579	0.0142 (0.0189)	0.0523 (0.0634)	0.136 (0.15)	0.0312 (0.0394)	0.00354 (0.00528)	0.0184 (0.0242)	0.492 (0.505)	0.355 (0.37)
del 3q11 1	98 (16%)	527	1e-05 (2.39e-05)	3e-05 (6.66e-05)	0.577 (0.587)	4e-05 (8.56e-05)	0.444 (0.456)	0.00352 (0.00526)	0.165 (0.178)	0.0723 (0.0848)
amp 8p11 21	272 (44%)	353	0.286 (0.302)	0.0235 (0.0302)	0.0195 (0.0256)	0.0797 (0.0925)	0.0978 (0.111)	0.00678 (0.00962)	0.438 (0.45)	0.384 (0.399)
amp 12q15	161 (26%)	464	1e-05 (2.39e-05)	0.0223 (0.0289)	0.537 (0.549)	0.918 (0.92)	0.0836 (0.0961)	0.0524 (0.0634)	0.0343 (0.0431)	0.403 (0.417)
del 2q32 1	87 (14%)	538	0.00093 (0.00158)	0.0088 (0.0121)	0.0648 (0.0775)	0.138 (0.153)	0.18 (0.194)	0.0233 (0.03)	0.15 (0.164)	0.367 (0.382)
del 17q24 3	103 (16%)	522	1e-05 (2.39e-05)	0.0822 (0.0951)	0.209 (0.224)	0.00955 (0.0131)	0.0376 (0.047)	0.0591 (0.0712)	0.67 (0.676)	0.603 (0.613)
del 20p12 1	72 (12%)	553	0.0001 (0.000198)	0.0275 (0.0351)	0.318 (0.333)	0.0828 (0.0956)	0.424 (0.437)	0.00317 (0.00478)	0.236 (0.25)	0.426 (0.438)
amp 10q22 2	125 (20%)	500	1e-05 (2.39e-05)	0.0507 (0.0617)	0.987 (0.988)	0.0225 (0.0292)	0.679 (0.684)	0.257 (0.272)	0.139 (0.153)	0.147 (0.162)
amp 9p24 1	91 (15%)	534	0.235 (0.25)	0.348 (0.364)	0.0841 (0.0964)	0.237 (0.251)	0.0345 (0.0433)	0.104 (0.117)	0.0828 (0.0956)	0.0682 (0.0809)
del 1q44	43 (7%)	582	0.0592 (0.0712)	0.011 (0.0149)	0.665 (0.672)	0.403 (0.417)	0.288 (0.304)	0.13 (0.144)	1 (1.00)	0.86 (0.864)

'amp_1p36.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 1(1P36.22) MUTATED	45	45	11
AMP PEAK 1(1P36.22) WILD-TYPE	121	165	238

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

'amp_1p36.22' versus 'METHLYATION_CNMF'

P value = 0.00622 (Fisher's exact test), Q value = 0.0089

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 1(1P36.22) MUTATED	40	36	17
AMP PEAK 1(1P36.22) WILD-TYPE	208	121	155

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

'amp_1p36.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0082 (Fisher's exact test), Q value = 0.011

Table S3. Gene #1: 'amp_1p36.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 1(1P36.22) MUTATED	17	23	7	12	8
AMP PEAK 1(1P36.22) WILD-TYPE	58	127	18	77	108

Figure S3. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.048

Table S4. Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 1(1P36.22) MUTATED	32	55	12
AMP PEAK 1(1P36.22) WILD-TYPE	132	273	119

Figure S4. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1p36.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0021

Table S5. Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 1(1P36.22) MUTATED	34	20	27	13	5
AMP PEAK 1(1P36.22) WILD-TYPE	93	85	202	82	62

Figure S5. Get High-res Image Gene #1: 'amp_1p36.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1p36.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.002

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 1(1P36.22) MUTATED	12	30	21	7	13
AMP PEAK 1(1P36.22) WILD-TYPE	35	92	141	94	79

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

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S7. Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 2(1P34.2) MUTATED	34	51	10
AMP PEAK 2(1P34.2) WILD-TYPE	132	159	239

Figure S7. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.0071

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 2(1P34.2) MUTATED	36	36	17
AMP PEAK 2(1P34.2) WILD-TYPE	212	121	155

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

'amp_1p34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.024

Table S9. Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 2(1P34.2) MUTATED	14	24	4	18	7
AMP PEAK 2(1P34.2) WILD-TYPE	61	126	21	71	109

Figure S9. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.042

Table S10. Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 2(1P34.2) MUTATED	33	50	12
AMP PEAK 2(1P34.2) WILD-TYPE	131	278	119

Figure S10. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00292 (Fisher's exact test), Q value = 0.0044

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 2(1P34.2) MUTATED	12	24	16	8	19
AMP PEAK 2(1P34.2) WILD-TYPE	35	98	146	93	73

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

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S12. Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 3(1Q21.3) MUTATED	98	121	30
AMP PEAK 3(1Q21.3) WILD-TYPE	68	89	219

Figure S12. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 3(1Q21.3) MUTATED	99	96	37
AMP PEAK 3(1Q21.3) WILD-TYPE	149	61	135

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 0.0087 (Fisher's exact test), Q value = 0.012

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 3(1Q21.3) MUTATED	103	59	25
AMP PEAK 3(1Q21.3) WILD-TYPE	131	70	67

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

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S15. Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 3(1Q21.3) MUTATED	44	62	11	44	26
AMP PEAK 3(1Q21.3) WILD-TYPE	31	88	14	45	90

Figure S15. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S16. Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 3(1Q21.3) MUTATED	81	134	32
AMP PEAK 3(1Q21.3) WILD-TYPE	83	194	99

Figure S16. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S17. Gene #3: 'amp_1q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 3(1Q21.3) MUTATED	75	45	64	46	17
AMP PEAK 3(1Q21.3) WILD-TYPE	52	60	165	49	50

Figure S17. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S18. Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 3(1Q21.3) MUTATED	76	83	48
AMP PEAK 3(1Q21.3) WILD-TYPE	68	126	123

Figure S18. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S19. Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 3(1Q21.3) MUTATED	25	64	46	27	45
AMP PEAK 3(1Q21.3) WILD-TYPE	22	58	116	74	47

Figure S19. Get High-res Image Gene #3: 'amp_1q21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q42.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S20. Gene #4: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 4(1Q42.3) MUTATED	97	116	31
AMP PEAK 4(1Q42.3) WILD-TYPE	69	94	218

Figure S20. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q42.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S21. Gene #4: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 4(1Q42.3) MUTATED	86	99	43
AMP PEAK 4(1Q42.3) WILD-TYPE	162	58	129

Figure S21. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.011

Table S22. Gene #4: 'amp_1q42.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 4(1Q42.3) MUTATED	96	63	26
AMP PEAK 4(1Q42.3) WILD-TYPE	138	66	66

Figure S22. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_1q42.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 4(1Q42.3) MUTATED	43	54	10	48	30
AMP PEAK 4(1Q42.3) WILD-TYPE	32	96	15	41	86

Figure S23. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S24. Gene #4: 'amp_1q42.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 4(1Q42.3) MUTATED	91	113	39
AMP PEAK 4(1Q42.3) WILD-TYPE	73	215	92

Figure S24. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_1q42.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S25. Gene #4: 'amp_1q42.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 4(1Q42.3) MUTATED	77	40	55	51	20
AMP PEAK 4(1Q42.3) WILD-TYPE	50	65	174	44	47

Figure S25. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S26. Gene #4: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 4(1Q42.3) MUTATED	82	73	52
AMP PEAK 4(1Q42.3) WILD-TYPE	62	136	119

Figure S26. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_1q42.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S27. Gene #4: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 4(1Q42.3) MUTATED	27	54	46	31	49
AMP PEAK 4(1Q42.3) WILD-TYPE	20	68	116	70	43

Figure S27. Get High-res Image Gene #4: 'amp_1q42.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S28. Gene #5: 'amp_2q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 5(2Q12.2) MUTATED	61	76	18
AMP PEAK 5(2Q12.2) WILD-TYPE	105	134	231

Figure S28. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_2q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S29. Gene #5: 'amp_2q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 5(2Q12.2) MUTATED	59	62	26
AMP PEAK 5(2Q12.2) WILD-TYPE	189	95	146

Figure S29. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_2q12.2' versus 'MRNASEQ_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00081

Table S30. Gene #5: 'amp_2q12.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 5(2Q12.2) MUTATED	59	48	13
AMP PEAK 5(2Q12.2) WILD-TYPE	175	81	79

Figure S30. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_2q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S31. Gene #5: 'amp_2q12.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 5(2Q12.2) MUTATED	25	32	9	37	17
AMP PEAK 5(2Q12.2) WILD-TYPE	50	118	16	52	99

Figure S31. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_2q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 5(2Q12.2) MUTATED	64	73	18
AMP PEAK 5(2Q12.2) WILD-TYPE	100	255	113

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

'amp_2q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S33. Gene #5: 'amp_2q12.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 5(2Q12.2) MUTATED	40	25	42	39	9
AMP PEAK 5(2Q12.2) WILD-TYPE	87	80	187	56	58

Figure S33. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_2q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S34. Gene #5: 'amp_2q12.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 5(2Q12.2) MUTATED	56	48	31
AMP PEAK 5(2Q12.2) WILD-TYPE	88	161	140

Figure S34. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_2q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S35. Gene #5: 'amp_2q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 5(2Q12.2) MUTATED	13	38	31	15	38
AMP PEAK 5(2Q12.2) WILD-TYPE	34	84	131	86	54

Figure S35. Get High-res Image Gene #5: 'amp_2q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S36. Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 6(3Q26.2) MUTATED	68	170	49
AMP PEAK 6(3Q26.2) WILD-TYPE	98	40	200

Figure S36. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S37. Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 6(3Q26.2) MUTATED	94	118	56
AMP PEAK 6(3Q26.2) WILD-TYPE	154	39	116

Figure S37. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S38. Gene #6: 'amp_3q26.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 6(3Q26.2) MUTATED	98	93	26
AMP PEAK 6(3Q26.2) WILD-TYPE	136	36	66

Figure S38. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S39. Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 6(3Q26.2) MUTATED	33	60	8	76	40
AMP PEAK 6(3Q26.2) WILD-TYPE	42	90	17	13	76

Figure S39. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S40. Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 6(3Q26.2) MUTATED	119	129	38
AMP PEAK 6(3Q26.2) WILD-TYPE	45	199	93

Figure S40. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 6(3Q26.2) MUTATED	61	40	85	82	18
AMP PEAK 6(3Q26.2) WILD-TYPE	66	65	144	13	49

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

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S42. Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 6(3Q26.2) MUTATED	104	79	63
AMP PEAK 6(3Q26.2) WILD-TYPE	40	130	108

Figure S42. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S43. Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 6(3Q26.2) MUTATED	23	54	60	29	80
AMP PEAK 6(3Q26.2) WILD-TYPE	24	68	102	72	12

Figure S43. Get High-res Image Gene #6: 'amp_3q26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S44. Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 7(5P15.33) MUTATED	85	116	27
AMP PEAK 7(5P15.33) WILD-TYPE	81	94	222

Figure S44. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S45. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 7(5P15.33) MUTATED	69	104	42
AMP PEAK 7(5P15.33) WILD-TYPE	179	53	130

Figure S45. Get High-res Image Gene #7: '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 = 2.4e-05

Table S46. Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 7(5P15.33) MUTATED	80	75	18
AMP PEAK 7(5P15.33) WILD-TYPE	154	54	74

Figure S46. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S47. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 7(5P15.33) MUTATED	39	46	5	60	23
AMP PEAK 7(5P15.33) WILD-TYPE	36	104	20	29	93

Figure S47. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S48. Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 7(5P15.33) MUTATED	96	102	29
AMP PEAK 7(5P15.33) WILD-TYPE	68	226	102

Figure S48. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S49. Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 7(5P15.33) MUTATED	69	24	57	64	13
AMP PEAK 7(5P15.33) WILD-TYPE	58	81	172	31	54

Figure S49. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 7(5P15.33) MUTATED	87	76	38
AMP PEAK 7(5P15.33) WILD-TYPE	57	133	133

Figure S50. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S51. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 7(5P15.33) MUTATED	23	48	48	19	63
AMP PEAK 7(5P15.33) WILD-TYPE	24	74	114	82	29

Figure S51. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S52. Gene #8: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 8(5P13.1) MUTATED	85	102	29
AMP PEAK 8(5P13.1) WILD-TYPE	81	108	220

Figure S52. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S53. Gene #8: 'amp_5p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 8(5P13.1) MUTATED	65	93	43
AMP PEAK 8(5P13.1) WILD-TYPE	183	64	129

Figure S53. Get High-res Image Gene #8: '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 = 2.4e-05

Table S54. Gene #8: 'amp_5p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 8(5P13.1) MUTATED	74	68	22
AMP PEAK 8(5P13.1) WILD-TYPE	160	61	70

Figure S54. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_5p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S55. Gene #8: 'amp_5p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 8(5P13.1) MUTATED	34	45	6	53	26
AMP PEAK 8(5P13.1) WILD-TYPE	41	105	19	36	90

Figure S55. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S56. Gene #8: 'amp_5p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 8(5P13.1) MUTATED	88	94	34
AMP PEAK 8(5P13.1) WILD-TYPE	76	234	97

Figure S56. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_5p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S57. Gene #8: 'amp_5p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 8(5P13.1) MUTATED	68	18	58	56	16
AMP PEAK 8(5P13.1) WILD-TYPE	59	87	171	39	51

Figure S57. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S58. Gene #8: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 8(5P13.1) MUTATED	78	66	46
AMP PEAK 8(5P13.1) WILD-TYPE	66	143	125

Figure S58. Get High-res Image Gene #8: 'amp_5p13.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_5p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 8(5P13.1) MUTATED	21	43	49	22	55
AMP PEAK 8(5P13.1) WILD-TYPE	26	79	113	79	37

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

'amp_6p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S60. Gene #9: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 9(6P21.1) MUTATED	94	74	24
AMP PEAK 9(6P21.1) WILD-TYPE	72	136	225

Figure S60. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S61. Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 9(6P21.1) MUTATED	80	69	27
AMP PEAK 9(6P21.1) WILD-TYPE	168	88	145

Figure S61. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.038

Table S62. Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 9(6P21.1) MUTATED	80	41	18
AMP PEAK 9(6P21.1) WILD-TYPE	154	88	74

Figure S62. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_6p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S63. Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 9(6P21.1) MUTATED	37	50	12	24	16
AMP PEAK 9(6P21.1) WILD-TYPE	38	100	13	65	100

Figure S63. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S64. Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 9(6P21.1) MUTATED	60	111	19
AMP PEAK 9(6P21.1) WILD-TYPE	104	217	112

Figure S64. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S65. Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 9(6P21.1) MUTATED	66	35	53	26	10
AMP PEAK 9(6P21.1) WILD-TYPE	61	70	176	69	57

Figure S65. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0032

Table S66. Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 9(6P21.1) MUTATED	58	70	38
AMP PEAK 9(6P21.1) WILD-TYPE	86	139	133

Figure S66. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6p21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S67. Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 9(6P21.1) MUTATED	26	60	38	16	26
AMP PEAK 9(6P21.1) WILD-TYPE	21	62	124	85	66

Figure S67. Get High-res Image Gene #9: 'amp_6p21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S68. Gene #10: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 10(6Q12) MUTATED	67	53	21
AMP PEAK 10(6Q12) WILD-TYPE	99	157	228

Figure S68. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S69. Gene #10: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 10(6Q12) MUTATED	55	55	17
AMP PEAK 10(6Q12) WILD-TYPE	193	102	155

Figure S69. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S70. Gene #10: 'amp_6q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 10(6Q12) MUTATED	31	35	10	21	10
AMP PEAK 10(6Q12) WILD-TYPE	44	115	15	68	106

Figure S70. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.00409 (Fisher's exact test), Q value = 0.006

Table S71. Gene #10: 'amp_6q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 10(6Q12) MUTATED	49	73	18
AMP PEAK 10(6Q12) WILD-TYPE	115	255	113

Figure S71. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S72. Gene #10: 'amp_6q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 10(6Q12) MUTATED	49	25	37	23	6
AMP PEAK 10(6Q12) WILD-TYPE	78	80	192	72	61

Figure S72. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00113 (Fisher's exact test), Q value = 0.0019

Table S73. Gene #10: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 10(6Q12) MUTATED	47	46	26
AMP PEAK 10(6Q12) WILD-TYPE	97	163	145

Figure S73. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_6q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S74. Gene #10: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 10(6Q12) MUTATED	24	36	25	12	22
AMP PEAK 10(6Q12) WILD-TYPE	23	86	137	89	70

Figure S74. Get High-res Image Gene #10: 'amp_6q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S75. Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 11(6Q21) MUTATED	57	34	20
AMP PEAK 11(6Q21) WILD-TYPE	109	176	229

Figure S75. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0034

Table S76. Gene #11: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 11(6Q21) MUTATED	43	38	17
AMP PEAK 11(6Q21) WILD-TYPE	205	119	155

Figure S76. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S77. Gene #11: 'amp_6q21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 11(6Q21) MUTATED	25	27	8	8	11
AMP PEAK 11(6Q21) WILD-TYPE	50	123	17	81	105

Figure S77. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S78. Gene #11: 'amp_6q21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 11(6Q21) MUTATED	45	20	31	9	5
AMP PEAK 11(6Q21) WILD-TYPE	82	85	198	86	62

Figure S78. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S79. Gene #11: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 11(6Q21) MUTATED	19	33	18	11	9
AMP PEAK 11(6Q21) WILD-TYPE	28	89	144	90	83

Figure S79. Get High-res Image Gene #11: 'amp_6q21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S80. Gene #12: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 12(7P22.3) MUTATED	128	148	77
AMP PEAK 12(7P22.3) WILD-TYPE	38	62	172

Figure S80. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S81. Gene #12: 'amp_7p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 12(7P22.3) MUTATED	154	106	67
AMP PEAK 12(7P22.3) WILD-TYPE	94	51	105

Figure S81. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p22.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S82. Gene #12: 'amp_7p22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 12(7P22.3) MUTATED	144	86	35
AMP PEAK 12(7P22.3) WILD-TYPE	90	43	57

Figure S82. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S83. Gene #12: 'amp_7p22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 12(7P22.3) MUTATED	56	87	15	59	48
AMP PEAK 12(7P22.3) WILD-TYPE	19	63	10	30	68

Figure S83. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7p22.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S84. Gene #12: 'amp_7p22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 12(7P22.3) MUTATED	111	190	51
AMP PEAK 12(7P22.3) WILD-TYPE	53	138	80

Figure S84. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S85. Gene #12: 'amp_7p22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 12(7P22.3) MUTATED	89	64	112	62	25
AMP PEAK 12(7P22.3) WILD-TYPE	38	41	117	33	42

Figure S85. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S86. Gene #12: 'amp_7p22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 12(7P22.3) MUTATED	102	120	77
AMP PEAK 12(7P22.3) WILD-TYPE	42	89	94

Figure S86. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S87. Gene #12: 'amp_7p22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 12(7P22.3) MUTATED	37	79	83	40	60
AMP PEAK 12(7P22.3) WILD-TYPE	10	43	79	61	32

Figure S87. Get High-res Image Gene #12: 'amp_7p22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S88. Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 13(7P11.2) MUTATED	117	143	80
AMP PEAK 13(7P11.2) WILD-TYPE	49	67	169

Figure S88. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S89. Gene #13: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 13(7P11.2) MUTATED	150	103	64
AMP PEAK 13(7P11.2) WILD-TYPE	98	54	108

Figure S89. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S90. Gene #13: 'amp_7p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 13(7P11.2) MUTATED	130	85	34
AMP PEAK 13(7P11.2) WILD-TYPE	104	44	58

Figure S90. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00059

Table S91. Gene #13: 'amp_7p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 13(7P11.2) MUTATED	48	79	19	57	46
AMP PEAK 13(7P11.2) WILD-TYPE	27	71	6	32	70

Figure S91. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S92. Gene #13: 'amp_7p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 13(7P11.2) MUTATED	105	183	50
AMP PEAK 13(7P11.2) WILD-TYPE	59	145	81

Figure S92. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00419 (Fisher's exact test), Q value = 0.0062

Table S93. Gene #13: 'amp_7p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 13(7P11.2) MUTATED	79	57	119	59	24
AMP PEAK 13(7P11.2) WILD-TYPE	48	48	110	36	43

Figure S93. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S94. Gene #13: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 13(7P11.2) MUTATED	100	113	72
AMP PEAK 13(7P11.2) WILD-TYPE	44	96	99

Figure S94. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S95. Gene #13: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 13(7P11.2) MUTATED	34	80	75	38	58
AMP PEAK 13(7P11.2) WILD-TYPE	13	42	87	63	34

Figure S95. Get High-res Image Gene #13: 'amp_7p11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S96. Gene #14: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 14(7Q21.2) MUTATED	99	139	79
AMP PEAK 14(7Q21.2) WILD-TYPE	67	71	170

Figure S96. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S97. Gene #14: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 14(7Q21.2) MUTATED	132	95	65
AMP PEAK 14(7Q21.2) WILD-TYPE	116	62	107

Figure S97. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S98. Gene #14: 'amp_7q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 14(7Q21.2) MUTATED	115	83	34
AMP PEAK 14(7Q21.2) WILD-TYPE	119	46	58

Figure S98. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0387 (Fisher's exact test), Q value = 0.048

Table S99. Gene #14: 'amp_7q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 14(7Q21.2) MUTATED	42	75	13	55	47
AMP PEAK 14(7Q21.2) WILD-TYPE	33	75	12	34	69

Figure S99. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 0.00324 (Fisher's exact test), Q value = 0.0049

Table S100. Gene #14: 'amp_7q21.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 14(7Q21.2) MUTATED	94	171	50
AMP PEAK 14(7Q21.2) WILD-TYPE	70	157	81

Figure S100. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00242 (Fisher's exact test), Q value = 0.0037

Table S101. Gene #14: 'amp_7q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 14(7Q21.2) MUTATED	68	61	103	59	24
AMP PEAK 14(7Q21.2) WILD-TYPE	59	44	126	36	43

Figure S101. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S102. Gene #14: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 14(7Q21.2) MUTATED	95	102	67
AMP PEAK 14(7Q21.2) WILD-TYPE	49	107	104

Figure S102. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00399 (Fisher's exact test), Q value = 0.0059

Table S103. Gene #14: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 14(7Q21.2) MUTATED	26	69	74	38	57
AMP PEAK 14(7Q21.2) WILD-TYPE	21	53	88	63	35

Figure S103. Get High-res Image Gene #14: 'amp_7q21.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p23.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S104. Gene #15: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 15(8P23.1) MUTATED	59	54	116
AMP PEAK 15(8P23.1) WILD-TYPE	107	156	133

Figure S104. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8p23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S105. Gene #15: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 15(8P23.1) MUTATED	119	33	54
AMP PEAK 15(8P23.1) WILD-TYPE	129	124	118

Figure S105. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S106. Gene #15: 'amp_8p23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 15(8P23.1) MUTATED	109	20	30
AMP PEAK 15(8P23.1) WILD-TYPE	125	109	62

Figure S106. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8p23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S107. Gene #15: 'amp_8p23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 15(8P23.1) MUTATED	18	74	2	17	48
AMP PEAK 15(8P23.1) WILD-TYPE	57	76	23	72	68

Figure S107. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S108. Gene #15: 'amp_8p23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 15(8P23.1) MUTATED	40	146	42
AMP PEAK 15(8P23.1) WILD-TYPE	124	182	89

Figure S108. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8p23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S109. Gene #15: 'amp_8p23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 15(8P23.1) MUTATED	44	54	88	18	24
AMP PEAK 15(8P23.1) WILD-TYPE	83	51	141	77	43

Figure S109. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S110. Gene #15: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 15(8P23.1) MUTATED	33	92	59
AMP PEAK 15(8P23.1) WILD-TYPE	111	117	112

Figure S110. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8p23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S111. Gene #15: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 15(8P23.1) MUTATED	11	53	64	40	16
AMP PEAK 15(8P23.1) WILD-TYPE	36	69	98	61	76

Figure S111. Get High-res Image Gene #15: 'amp_8p23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.03

Table S112. Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 16(8P11.21) MUTATED	120	68	60
AMP PEAK 16(8P11.21) WILD-TYPE	128	89	112

Figure S112. Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.026

Table S113. Gene #16: 'amp_8p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 16(8P11.21) MUTATED	114	51	30
AMP PEAK 16(8P11.21) WILD-TYPE	120	78	62

Figure S113. Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00678 (Fisher's exact test), Q value = 0.0096

Table S114. Gene #16: 'amp_8p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 16(8P11.21) MUTATED	52	61	94	43	21
AMP PEAK 16(8P11.21) WILD-TYPE	75	44	135	52	46

Figure S114. Get High-res Image Gene #16: 'amp_8p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S115. Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 17(8Q24.21) MUTATED	143	164	147
AMP PEAK 17(8Q24.21) WILD-TYPE	23	46	102

Figure S115. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S116. Gene #17: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 17(8Q24.21) MUTATED	186	132	99
AMP PEAK 17(8Q24.21) WILD-TYPE	62	25	73

Figure S116. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00064

Table S117. Gene #17: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 17(8Q24.21) MUTATED	170	100	49
AMP PEAK 17(8Q24.21) WILD-TYPE	64	29	43

Figure S117. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S118. Gene #17: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 17(8Q24.21) MUTATED	63	107	14	73	62
AMP PEAK 17(8Q24.21) WILD-TYPE	12	43	11	16	54

Figure S118. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S119. Gene #17: 'amp_8q24.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 17(8Q24.21) MUTATED	140	238	74
AMP PEAK 17(8Q24.21) WILD-TYPE	24	90	57

Figure S119. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S120. Gene #17: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 17(8Q24.21) MUTATED	106	86	147	78	35
AMP PEAK 17(8Q24.21) WILD-TYPE	21	19	82	17	32

Figure S120. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S121. Gene #17: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 17(8Q24.21) MUTATED	121	150	109
AMP PEAK 17(8Q24.21) WILD-TYPE	23	59	62

Figure S121. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S122. Gene #17: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 17(8Q24.21) MUTATED	40	101	104	61	74
AMP PEAK 17(8Q24.21) WILD-TYPE	7	21	58	40	18

Figure S122. Get High-res Image Gene #17: 'amp_8q24.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.1' versus 'MIRSEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.043

Table S123. Gene #18: 'amp_9p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 18(9P24.1) MUTATED	34	41	15
AMP PEAK 18(9P24.1) WILD-TYPE	130	287	116

Figure S123. Get High-res Image Gene #18: 'amp_9p24.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00062

Table S124. Gene #19: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 19(9P13.3) MUTATED	50	47	35
AMP PEAK 19(9P13.3) WILD-TYPE	116	163	214

Figure S124. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.005

Table S125. Gene #19: 'amp_9p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 19(9P13.3) MUTATED	53	28	7
AMP PEAK 19(9P13.3) WILD-TYPE	181	101	85

Figure S125. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.033

Table S126. Gene #19: 'amp_9p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 19(9P13.3) MUTATED	45	68	19
AMP PEAK 19(9P13.3) WILD-TYPE	119	260	112

Figure S126. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.0096

Table S127. Gene #19: 'amp_9p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 19(9P13.3) MUTATED	16	36	30	13	19
AMP PEAK 19(9P13.3) WILD-TYPE	31	86	132	88	73

Figure S127. Get High-res Image Gene #19: 'amp_9p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S128. Gene #20: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 20(9Q34.3) MUTATED	68	78	39
AMP PEAK 20(9Q34.3) WILD-TYPE	98	132	210

Figure S128. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.0064

Table S129. Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 20(9Q34.3) MUTATED	71	61	38
AMP PEAK 20(9Q34.3) WILD-TYPE	177	96	134

Figure S129. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0037

Table S130. Gene #20: 'amp_9q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 20(9Q34.3) MUTATED	61	49	16
AMP PEAK 20(9Q34.3) WILD-TYPE	173	80	76

Figure S130. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.015

Table S131. Gene #20: 'amp_9q34.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 20(9Q34.3) MUTATED	62	93	29
AMP PEAK 20(9Q34.3) WILD-TYPE	102	235	102

Figure S131. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.024

Table S132. Gene #20: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 20(9Q34.3) MUTATED	54	54	41
AMP PEAK 20(9Q34.3) WILD-TYPE	90	155	130

Figure S132. Get High-res Image Gene #20: 'amp_9q34.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_10p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S133. Gene #21: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 21(10P11.22) MUTATED	75	65	29
AMP PEAK 21(10P11.22) WILD-TYPE	91	145	220

Figure S133. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10p11.22' versus 'METHLYATION_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0032

Table S134. Gene #21: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 21(10P11.22) MUTATED	72	54	31
AMP PEAK 21(10P11.22) WILD-TYPE	176	103	141

Figure S134. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_10p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00481 (Fisher's exact test), Q value = 0.007

Table S135. Gene #21: 'amp_10p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 21(10P11.22) MUTATED	33	38	7	19	23
AMP PEAK 21(10P11.22) WILD-TYPE	42	112	18	70	93

Figure S135. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S136. Gene #21: 'amp_10p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 21(10P11.22) MUTATED	56	29	50	21	12
AMP PEAK 21(10P11.22) WILD-TYPE	71	76	179	74	55

Figure S136. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_10p11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.027

Table S137. Gene #21: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 21(10P11.22) MUTATED	15	47	36	23	22
AMP PEAK 21(10P11.22) WILD-TYPE	32	75	126	78	70

Figure S137. Get High-res Image Gene #21: 'amp_10p11.22' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S138. Gene #22: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 22(10Q22.2) MUTATED	43	56	26
AMP PEAK 22(10Q22.2) WILD-TYPE	123	154	223

Figure S138. Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0225 (Fisher's exact test), Q value = 0.029

Table S139. Gene #22: 'amp_10q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 22(10Q22.2) MUTATED	25	29	5	11	21
AMP PEAK 22(10Q22.2) WILD-TYPE	50	121	20	78	95

Figure S139. Get High-res Image Gene #22: 'amp_10q22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S140. Gene #23: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 23(10Q26.13) MUTATED	48	42	29
AMP PEAK 23(10Q26.13) WILD-TYPE	118	168	220

Figure S140. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_10q26.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S141. Gene #23: 'amp_10q26.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 23(10Q26.13) MUTATED	26	25	7	6	21
AMP PEAK 23(10Q26.13) WILD-TYPE	49	125	18	83	95

Figure S141. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.019

Table S142. Gene #23: 'amp_10q26.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 23(10Q26.13) MUTATED	20	65	33
AMP PEAK 23(10Q26.13) WILD-TYPE	144	263	98

Figure S142. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_10q26.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00329 (Fisher's exact test), Q value = 0.0049

Table S143. Gene #23: 'amp_10q26.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 23(10Q26.13) MUTATED	37	18	42	8	13
AMP PEAK 23(10Q26.13) WILD-TYPE	90	87	187	87	54

Figure S143. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_10q26.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.0038

Table S144. Gene #23: 'amp_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 23(10Q26.13) MUTATED	10	33	30	20	6
AMP PEAK 23(10Q26.13) WILD-TYPE	37	89	132	81	86

Figure S144. Get High-res Image Gene #23: 'amp_10q26.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S145. Gene #24: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 24(11P13) MUTATED	55	60	23
AMP PEAK 24(11P13) WILD-TYPE	111	150	226

Figure S145. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11p13' versus 'METHLYATION_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0027

Table S146. Gene #24: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 24(11P13) MUTATED	49	51	29
AMP PEAK 24(11P13) WILD-TYPE	199	106	143

Figure S146. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00809 (Fisher's exact test), Q value = 0.011

Table S147. Gene #24: 'amp_11p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 24(11P13) MUTATED	21	18	6	25	27
AMP PEAK 24(11P13) WILD-TYPE	54	132	19	64	89

Figure S147. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00187 (Fisher's exact test), Q value = 0.003

Table S148. Gene #24: 'amp_11p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 24(11P13) MUTATED	41	17	38	28	12
AMP PEAK 24(11P13) WILD-TYPE	86	88	191	67	55

Figure S148. Get High-res Image Gene #24: 'amp_11p13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S149. Gene #25: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 25(11Q13.3) MUTATED	73	116	29
AMP PEAK 25(11Q13.3) WILD-TYPE	93	94	220

Figure S149. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S150. Gene #25: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 25(11Q13.3) MUTATED	76	88	41
AMP PEAK 25(11Q13.3) WILD-TYPE	172	69	131

Figure S150. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S151. Gene #25: 'amp_11q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 25(11Q13.3) MUTATED	69	83	10
AMP PEAK 25(11Q13.3) WILD-TYPE	165	46	82

Figure S151. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S152. Gene #25: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 25(11Q13.3) MUTATED	33	35	11	63	20
AMP PEAK 25(11Q13.3) WILD-TYPE	42	115	14	26	96

Figure S152. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S153. Gene #25: 'amp_11q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 25(11Q13.3) MUTATED	94	102	21
AMP PEAK 25(11Q13.3) WILD-TYPE	70	226	110

Figure S153. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S154. Gene #25: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 25(11Q13.3) MUTATED	48	31	60	68	10
AMP PEAK 25(11Q13.3) WILD-TYPE	79	74	169	27	57

Figure S154. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S155. Gene #25: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 25(11Q13.3) MUTATED	83	66	43
AMP PEAK 25(11Q13.3) WILD-TYPE	61	143	128

Figure S155. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S156. Gene #25: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 25(11Q13.3) MUTATED	17	47	42	20	66
AMP PEAK 25(11Q13.3) WILD-TYPE	30	75	120	81	26

Figure S156. Get High-res Image Gene #25: 'amp_11q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S157. Gene #26: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 26(12P12.1) MUTATED	48	113	46
AMP PEAK 26(12P12.1) WILD-TYPE	118	97	203

Figure S157. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S158. Gene #26: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 26(12P12.1) MUTATED	73	79	46
AMP PEAK 26(12P12.1) WILD-TYPE	175	78	126

Figure S158. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0022

Table S159. Gene #26: 'amp_12p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 26(12P12.1) MUTATED	66	60	26
AMP PEAK 26(12P12.1) WILD-TYPE	168	69	66

Figure S159. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0011

Table S160. Gene #26: 'amp_12p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 26(12P12.1) MUTATED	25	39	8	47	33
AMP PEAK 26(12P12.1) WILD-TYPE	50	111	17	42	83

Figure S160. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S161. Gene #26: 'amp_12p12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 26(12P12.1) MUTATED	78	94	34
AMP PEAK 26(12P12.1) WILD-TYPE	86	234	97

Figure S161. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S162. Gene #26: 'amp_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 26(12P12.1) MUTATED	44	24	79	47	12
AMP PEAK 26(12P12.1) WILD-TYPE	83	81	150	48	55

Figure S162. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00046

Table S163. Gene #26: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 26(12P12.1) MUTATED	69	63	47
AMP PEAK 26(12P12.1) WILD-TYPE	75	146	124

Figure S163. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00209 (Fisher's exact test), Q value = 0.0033

Table S164. Gene #26: 'amp_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 26(12P12.1) MUTATED	17	42	48	25	47
AMP PEAK 26(12P12.1) WILD-TYPE	30	80	114	76	45

Figure S164. Get High-res Image Gene #26: 'amp_12p12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S165. Gene #27: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 27(12Q15) MUTATED	35	86	40
AMP PEAK 27(12Q15) WILD-TYPE	131	124	209

Figure S165. Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #1: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.0223 (Fisher's exact test), Q value = 0.029

Table S166. Gene #27: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 27(12Q15) MUTATED	56	54	40
AMP PEAK 27(12Q15) WILD-TYPE	192	103	132

Figure S166. Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_12q15' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.043

Table S167. Gene #27: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 27(12Q15) MUTATED	45	53	32
AMP PEAK 27(12Q15) WILD-TYPE	99	156	139

Figure S167. Get High-res Image Gene #27: 'amp_12q15' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S168. Gene #28: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 28(13Q12.3) MUTATED	120	43	53
AMP PEAK 28(13Q12.3) WILD-TYPE	46	167	196

Figure S168. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S169. Gene #28: 'amp_13q12.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 28(13Q12.3) MUTATED	103	24	20
AMP PEAK 28(13Q12.3) WILD-TYPE	131	105	72

Figure S169. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S170. Gene #28: 'amp_13q12.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 28(13Q12.3) MUTATED	36	62	12	9	28
AMP PEAK 28(13Q12.3) WILD-TYPE	39	88	13	80	88

Figure S170. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.014

Table S171. Gene #28: 'amp_13q12.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 28(13Q12.3) MUTATED	45	131	39
AMP PEAK 28(13Q12.3) WILD-TYPE	119	197	92

Figure S171. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_13q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S172. Gene #28: 'amp_13q12.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 28(13Q12.3) MUTATED	72	42	73	9	19
AMP PEAK 28(13Q12.3) WILD-TYPE	55	63	156	86	48

Figure S172. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_13q12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S173. Gene #28: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 28(13Q12.3) MUTATED	28	47	53	39	9
AMP PEAK 28(13Q12.3) WILD-TYPE	19	75	109	62	83

Figure S173. Get High-res Image Gene #28: 'amp_13q12.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S174. Gene #29: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 29(13Q22.1) MUTATED	131	55	57
AMP PEAK 29(13Q22.1) WILD-TYPE	35	155	192

Figure S174. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q22.1' versus 'METHLYATION_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0035

Table S175. Gene #29: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 29(13Q22.1) MUTATED	101	72	48
AMP PEAK 29(13Q22.1) WILD-TYPE	147	85	124

Figure S175. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S176. Gene #29: 'amp_13q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 29(13Q22.1) MUTATED	104	43	18
AMP PEAK 29(13Q22.1) WILD-TYPE	130	86	74

Figure S176. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_13q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S177. Gene #29: 'amp_13q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 29(13Q22.1) MUTATED	50	56	12	17	30
AMP PEAK 29(13Q22.1) WILD-TYPE	25	94	13	72	86

Figure S177. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S178. Gene #29: 'amp_13q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 29(13Q22.1) MUTATED	80	45	77	20	19
AMP PEAK 29(13Q22.1) WILD-TYPE	47	60	152	75	48

Figure S178. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_13q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S179. Gene #29: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 29(13Q22.1) MUTATED	36	53	58	35	19
AMP PEAK 29(13Q22.1) WILD-TYPE	11	69	104	66	73

Figure S179. Get High-res Image Gene #29: 'amp_13q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S180. Gene #30: 'amp_14q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 30(14Q13.3) MUTATED	34	69	10
AMP PEAK 30(14Q13.3) WILD-TYPE	132	141	239

Figure S180. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_14q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S181. Gene #30: 'amp_14q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 30(14Q13.3) MUTATED	34	53	20
AMP PEAK 30(14Q13.3) WILD-TYPE	214	104	152

Figure S181. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S182. Gene #30: 'amp_14q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 30(14Q13.3) MUTATED	29	45	8
AMP PEAK 30(14Q13.3) WILD-TYPE	205	84	84

Figure S182. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S183. Gene #30: 'amp_14q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 30(14Q13.3) MUTATED	13	20	3	39	7
AMP PEAK 30(14Q13.3) WILD-TYPE	62	130	22	50	109

Figure S183. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S184. Gene #30: 'amp_14q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 30(14Q13.3) MUTATED	54	45	13
AMP PEAK 30(14Q13.3) WILD-TYPE	110	283	118

Figure S184. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_14q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S185. Gene #30: 'amp_14q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 30(14Q13.3) MUTATED	22	16	24	41	9
AMP PEAK 30(14Q13.3) WILD-TYPE	105	89	205	54	58

Figure S185. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S186. Gene #30: 'amp_14q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 30(14Q13.3) MUTATED	46	27	26
AMP PEAK 30(14Q13.3) WILD-TYPE	98	182	145

Figure S186. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_14q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S187. Gene #30: 'amp_14q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 30(14Q13.3) MUTATED	8	24	16	10	41
AMP PEAK 30(14Q13.3) WILD-TYPE	39	98	146	91	51

Figure S187. Get High-res Image Gene #30: 'amp_14q13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S188. Gene #31: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 31(15Q26.1) MUTATED	67	75	26
AMP PEAK 31(15Q26.1) WILD-TYPE	99	135	223

Figure S188. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.00086

Table S189. Gene #31: 'amp_15q26.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 31(15Q26.1) MUTATED	69	40	10
AMP PEAK 31(15Q26.1) WILD-TYPE	165	89	82

Figure S189. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_15q26.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S190. Gene #31: 'amp_15q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 31(15Q26.1) MUTATED	33	41	12	19	14
AMP PEAK 31(15Q26.1) WILD-TYPE	42	109	13	70	102

Figure S190. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

Table S191. Gene #31: 'amp_15q26.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 31(15Q26.1) MUTATED	58	88	21
AMP PEAK 31(15Q26.1) WILD-TYPE	106	240	110

Figure S191. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_15q26.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

Table S192. Gene #31: 'amp_15q26.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 31(15Q26.1) MUTATED	50	25	64	21	7
AMP PEAK 31(15Q26.1) WILD-TYPE	77	80	165	74	60

Figure S192. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.06

Table S193. Gene #31: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 31(15Q26.1) MUTATED	47	65	37
AMP PEAK 31(15Q26.1) WILD-TYPE	97	144	134

Figure S193. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00056

Table S194. Gene #31: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 31(15Q26.1) MUTATED	18	51	42	17	21
AMP PEAK 31(15Q26.1) WILD-TYPE	29	71	120	84	71

Figure S194. Get High-res Image Gene #31: 'amp_15q26.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S195. Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 32(17Q12) MUTATED	98	87	37
AMP PEAK 32(17Q12) WILD-TYPE	68	123	212

Figure S195. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00041

Table S196. Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 32(17Q12) MUTATED	95	71	42
AMP PEAK 32(17Q12) WILD-TYPE	153	86	130

Figure S196. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 0.00646 (Fisher's exact test), Q value = 0.0092

Table S197. Gene #32: 'amp_17q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 32(17Q12) MUTATED	91	44	19
AMP PEAK 32(17Q12) WILD-TYPE	143	85	73

Figure S197. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00477 (Fisher's exact test), Q value = 0.0069

Table S198. Gene #32: 'amp_17q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 32(17Q12) MUTATED	38	49	11	27	29
AMP PEAK 32(17Q12) WILD-TYPE	37	101	14	62	87

Figure S198. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.0312 (Fisher's exact test), Q value = 0.039

Table S199. Gene #32: 'amp_17q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 32(17Q12) MUTATED	68	117	35
AMP PEAK 32(17Q12) WILD-TYPE	96	211	96

Figure S199. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.00096

Table S200. Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 32(17Q12) MUTATED	63	35	80	29	13
AMP PEAK 32(17Q12) WILD-TYPE	64	70	149	66	54

Figure S200. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S201. Gene #32: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 32(17Q12) MUTATED	23	58	56	21	28
AMP PEAK 32(17Q12) WILD-TYPE	24	64	106	80	64

Figure S201. Get High-res Image Gene #32: 'amp_17q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S202. Gene #33: 'amp_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 33(18P11.32) MUTATED	55	90	33
AMP PEAK 33(18P11.32) WILD-TYPE	111	120	216

Figure S202. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S203. Gene #33: 'amp_18p11.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 33(18P11.32) MUTATED	49	78	41
AMP PEAK 33(18P11.32) WILD-TYPE	199	79	131

Figure S203. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.0013

Table S204. Gene #33: 'amp_18p11.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 33(18P11.32) MUTATED	62	50	15
AMP PEAK 33(18P11.32) WILD-TYPE	172	79	77

Figure S204. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S205. Gene #33: 'amp_18p11.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 33(18P11.32) MUTATED	28	40	6	38	15
AMP PEAK 33(18P11.32) WILD-TYPE	47	110	19	51	101

Figure S205. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S206. Gene #33: 'amp_18p11.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 33(18P11.32) MUTATED	68	86	22
AMP PEAK 33(18P11.32) WILD-TYPE	96	242	109

Figure S206. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_18p11.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S207. Gene #33: 'amp_18p11.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 33(18P11.32) MUTATED	51	26	50	42	7
AMP PEAK 33(18P11.32) WILD-TYPE	76	79	179	53	60

Figure S207. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0012

Table S208. Gene #33: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 33(18P11.32) MUTATED	57	61	34
AMP PEAK 33(18P11.32) WILD-TYPE	87	148	137

Figure S208. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.00083

Table S209. Gene #33: 'amp_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 33(18P11.32) MUTATED	17	40	37	18	40
AMP PEAK 33(18P11.32) WILD-TYPE	30	82	125	83	52

Figure S209. Get High-res Image Gene #33: 'amp_18p11.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S210. Gene #34: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 34(18Q11.2) MUTATED	76	77	45
AMP PEAK 34(18Q11.2) WILD-TYPE	90	133	204

Figure S210. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.054

Table S211. Gene #34: 'amp_18q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 34(18Q11.2) MUTATED	78	37	18
AMP PEAK 34(18Q11.2) WILD-TYPE	156	92	74

Figure S211. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0012

Table S212. Gene #34: 'amp_18q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 34(18Q11.2) MUTATED	30	52	11	19	21
AMP PEAK 34(18Q11.2) WILD-TYPE	45	98	14	70	95

Figure S212. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

Table S213. Gene #34: 'amp_18q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 34(18Q11.2) MUTATED	60	34	69	21	14
AMP PEAK 34(18Q11.2) WILD-TYPE	67	71	160	74	53

Figure S213. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00974 (Fisher's exact test), Q value = 0.013

Table S214. Gene #34: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 34(18Q11.2) MUTATED	18	51	48	25	20
AMP PEAK 34(18Q11.2) WILD-TYPE	29	71	114	76	72

Figure S214. Get High-res Image Gene #34: 'amp_18q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S215. Gene #35: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 35(19P13.2) MUTATED	28	39	12
AMP PEAK 35(19P13.2) WILD-TYPE	138	171	237

Figure S215. Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0024

Table S216. Gene #35: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 35(19P13.2) MUTATED	31	32	12
AMP PEAK 35(19P13.2) WILD-TYPE	217	125	160

Figure S216. Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.048

Table S217. Gene #35: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 35(19P13.2) MUTATED	24	28	13
AMP PEAK 35(19P13.2) WILD-TYPE	120	181	158

Figure S217. Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.046

Table S218. Gene #35: 'amp_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 35(19P13.2) MUTATED	4	19	18	6	18
AMP PEAK 35(19P13.2) WILD-TYPE	43	103	144	95	74

Figure S218. Get High-res Image Gene #35: 'amp_19p13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S219. Gene #36: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 36(19Q12) MUTATED	86	75	24
AMP PEAK 36(19Q12) WILD-TYPE	80	135	225

Figure S219. Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S220. Gene #36: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 36(19Q12) MUTATED	63	69	41
AMP PEAK 36(19Q12) WILD-TYPE	185	88	131

Figure S220. Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S221. Gene #36: 'amp_19q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 36(19Q12) MUTATED	44	36	7	21	26
AMP PEAK 36(19Q12) WILD-TYPE	31	114	18	68	90

Figure S221. Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.02

Table S222. Gene #36: 'amp_19q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 36(19Q12) MUTATED	63	88	33
AMP PEAK 36(19Q12) WILD-TYPE	101	240	98

Figure S222. Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S223. Gene #36: 'amp_19q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 36(19Q12) MUTATED	82	22	45	23	12
AMP PEAK 36(19Q12) WILD-TYPE	45	83	184	72	55

Figure S223. Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S224. Gene #36: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 36(19Q12) MUTATED	33	40	38	25	22
AMP PEAK 36(19Q12) WILD-TYPE	14	82	124	76	70

Figure S224. Get High-res Image Gene #36: 'amp_19q12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S225. Gene #37: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 37(19Q13.43) MUTATED	62	71	31
AMP PEAK 37(19Q13.43) WILD-TYPE	104	139	218

Figure S225. Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #1: 'CN_CNMF'

'amp_19q13.43' versus 'METHLYATION_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.052

Table S226. Gene #37: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 37(19Q13.43) MUTATED	70	49	34
AMP PEAK 37(19Q13.43) WILD-TYPE	178	108	138

Figure S226. Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0025 (Fisher's exact test), Q value = 0.0038

Table S227. Gene #37: 'amp_19q13.43' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 37(19Q13.43) MUTATED	51	24	52	24	12
AMP PEAK 37(19Q13.43) WILD-TYPE	76	81	177	71	55

Figure S227. Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0046

Table S228. Gene #37: 'amp_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 37(19Q13.43) MUTATED	49	58	30
AMP PEAK 37(19Q13.43) WILD-TYPE	95	151	141

Figure S228. Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00179 (Fisher's exact test), Q value = 0.0029

Table S229. Gene #37: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 37(19Q13.43) MUTATED	23	37	37	18	22
AMP PEAK 37(19Q13.43) WILD-TYPE	24	85	125	83	70

Figure S229. Get High-res Image Gene #37: 'amp_19q13.43' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S230. Gene #38: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 38(20Q13.2) MUTATED	153	154	109
AMP PEAK 38(20Q13.2) WILD-TYPE	13	56	140

Figure S230. Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0028

Table S231. Gene #38: 'amp_20q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 38(20Q13.2) MUTATED	171	78	50
AMP PEAK 38(20Q13.2) WILD-TYPE	63	51	42

Figure S231. Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S232. Gene #38: 'amp_20q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 38(20Q13.2) MUTATED	68	98	18	46	69
AMP PEAK 38(20Q13.2) WILD-TYPE	7	52	7	43	47

Figure S232. Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S233. Gene #38: 'amp_20q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 38(20Q13.2) MUTATED	119	62	147	50	36
AMP PEAK 38(20Q13.2) WILD-TYPE	8	43	82	45	31

Figure S233. Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S234. Gene #38: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 38(20Q13.2) MUTATED	45	96	93	62	49
AMP PEAK 38(20Q13.2) WILD-TYPE	2	26	69	39	43

Figure S234. Get High-res Image Gene #38: 'amp_20q13.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S235. Gene #39: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
AMP PEAK 39(XQ28) MUTATED	47	78	29
AMP PEAK 39(XQ28) WILD-TYPE	119	132	220

Figure S235. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #1: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S236. Gene #39: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
AMP PEAK 39(XQ28) MUTATED	65	55	24
AMP PEAK 39(XQ28) WILD-TYPE	183	102	148

Figure S236. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S237. Gene #39: 'amp_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
AMP PEAK 39(XQ28) MUTATED	53	56	8
AMP PEAK 39(XQ28) WILD-TYPE	181	73	84

Figure S237. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S238. Gene #39: 'amp_xq28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
AMP PEAK 39(XQ28) MUTATED	22	31	8	42	14
AMP PEAK 39(XQ28) WILD-TYPE	53	119	17	47	102

Figure S238. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S239. Gene #39: 'amp_xq28' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
AMP PEAK 39(XQ28) MUTATED	62	76	15
AMP PEAK 39(XQ28) WILD-TYPE	102	252	116

Figure S239. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S240. Gene #39: 'amp_xq28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
AMP PEAK 39(XQ28) MUTATED	29	28	42	45	9
AMP PEAK 39(XQ28) WILD-TYPE	98	77	187	50	58

Figure S240. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.003 (Fisher's exact test), Q value = 0.0045

Table S241. Gene #39: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
AMP PEAK 39(XQ28) MUTATED	51	47	33
AMP PEAK 39(XQ28) WILD-TYPE	93	162	138

Figure S241. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'amp_xq28' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S242. Gene #39: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
AMP PEAK 39(XQ28) MUTATED	6	38	29	14	44
AMP PEAK 39(XQ28) WILD-TYPE	41	84	133	87	48

Figure S242. Get High-res Image Gene #39: 'amp_xq28' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S243. Gene #40: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 1(1P36.11) MUTATED	90	98	22
DEL PEAK 1(1P36.11) WILD-TYPE	76	112	227

Figure S243. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00056

Table S244. Gene #40: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 1(1P36.11) MUTATED	85	68	39
DEL PEAK 1(1P36.11) WILD-TYPE	163	89	133

Figure S244. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S245. Gene #40: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 1(1P36.11) MUTATED	91	47	13
DEL PEAK 1(1P36.11) WILD-TYPE	143	82	79

Figure S245. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.0011

Table S246. Gene #40: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 1(1P36.11) MUTATED	36	54	9	30	22
DEL PEAK 1(1P36.11) WILD-TYPE	39	96	16	59	94

Figure S246. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S247. Gene #40: 'del_1p36.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 1(1P36.11) MUTATED	64	120	25
DEL PEAK 1(1P36.11) WILD-TYPE	100	208	106

Figure S247. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S248. Gene #40: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 1(1P36.11) MUTATED	64	35	69	30	11
DEL PEAK 1(1P36.11) WILD-TYPE	63	70	160	65	56

Figure S248. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00243 (Fisher's exact test), Q value = 0.0037

Table S249. Gene #40: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 1(1P36.11) MUTATED	61	76	42
DEL PEAK 1(1P36.11) WILD-TYPE	83	133	129

Figure S249. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00063 (Fisher's exact test), Q value = 0.0011

Table S250. Gene #40: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 1(1P36.11) MUTATED	24	55	44	25	31
DEL PEAK 1(1P36.11) WILD-TYPE	23	67	118	76	61

Figure S250. Get High-res Image Gene #40: 'del_1p36.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S251. Gene #41: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 2(1P13.2) MUTATED	68	77	11
DEL PEAK 2(1P13.2) WILD-TYPE	98	133	238

Figure S251. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S252. Gene #41: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 2(1P13.2) MUTATED	64	68	15
DEL PEAK 2(1P13.2) WILD-TYPE	184	89	157

Figure S252. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p13.2' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S253. Gene #41: 'del_1p13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 2(1P13.2) MUTATED	58	45	10
DEL PEAK 2(1P13.2) WILD-TYPE	176	84	82

Figure S253. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_1p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S254. Gene #41: 'del_1p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 2(1P13.2) MUTATED	24	36	9	31	13
DEL PEAK 2(1P13.2) WILD-TYPE	51	114	16	58	103

Figure S254. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.015

Table S255. Gene #41: 'del_1p13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 2(1P13.2) MUTATED	48	87	20
DEL PEAK 2(1P13.2) WILD-TYPE	116	241	111

Figure S255. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0027

Table S256. Gene #41: 'del_1p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 2(1P13.2) MUTATED	40	21	54	33	7
DEL PEAK 2(1P13.2) WILD-TYPE	87	84	175	62	60

Figure S256. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.0078

Table S257. Gene #41: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 2(1P13.2) MUTATED	50	54	32
DEL PEAK 2(1P13.2) WILD-TYPE	94	155	139

Figure S257. Get High-res Image Gene #41: 'del_1p13.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_1q44' versus 'CN_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.019

Table S258. Gene #42: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 3(1Q44) MUTATED	19	17	10
DEL PEAK 3(1Q44) WILD-TYPE	147	193	239

Figure S258. Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'del_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.039

Table S259. Gene #42: 'del_1q44' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 3(1Q44) MUTATED	12	12	3	6	4
DEL PEAK 3(1Q44) WILD-TYPE	63	138	22	83	112

Figure S259. Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_1q44' versus 'MIRSEQ_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.0053

Table S260. Gene #42: 'del_1q44' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 3(1Q44) MUTATED	12	32	2
DEL PEAK 3(1Q44) WILD-TYPE	152	296	129

Figure S260. Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.024

Table S261. Gene #42: 'del_1q44' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 3(1Q44) MUTATED	14	5	21	6	0
DEL PEAK 3(1Q44) WILD-TYPE	113	100	208	89	67

Figure S261. Get High-res Image Gene #42: 'del_1q44' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_1q44' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.015

Table S262. Gene #43: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 4(1Q44) MUTATED	21	17	5
DEL PEAK 4(1Q44) WILD-TYPE	227	140	167

Figure S262. Get High-res Image Gene #43: 'del_1q44' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S263. Gene #44: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 5(2Q22.1) MUTATED	34	74	18
DEL PEAK 5(2Q22.1) WILD-TYPE	132	136	231

Figure S263. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S264. Gene #44: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 5(2Q22.1) MUTATED	31	68	20
DEL PEAK 5(2Q22.1) WILD-TYPE	217	89	152

Figure S264. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S265. Gene #44: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 5(2Q22.1) MUTATED	29	55	6
DEL PEAK 5(2Q22.1) WILD-TYPE	205	74	86

Figure S265. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S266. Gene #44: 'del_2q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 5(2Q22.1) MUTATED	16	18	6	43	7
DEL PEAK 5(2Q22.1) WILD-TYPE	59	132	19	46	109

Figure S266. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S267. Gene #44: 'del_2q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 5(2Q22.1) MUTATED	60	54	12
DEL PEAK 5(2Q22.1) WILD-TYPE	104	274	119

Figure S267. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S268. Gene #44: 'del_2q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 5(2Q22.1) MUTATED	31	7	37	46	5
DEL PEAK 5(2Q22.1) WILD-TYPE	96	98	192	49	62

Figure S268. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S269. Gene #44: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 5(2Q22.1) MUTATED	58	31	20
DEL PEAK 5(2Q22.1) WILD-TYPE	86	178	151

Figure S269. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S270. Gene #44: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 5(2Q22.1) MUTATED	10	25	17	11	46
DEL PEAK 5(2Q22.1) WILD-TYPE	37	97	145	90	46

Figure S270. Get High-res Image Gene #44: 'del_2q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q32.1' versus 'CN_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0016

Table S271. Gene #45: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 6(2Q32.1) MUTATED	34	33	20
DEL PEAK 6(2Q32.1) WILD-TYPE	132	177	229

Figure S271. Get High-res Image Gene #45: 'del_2q32.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q32.1' versus 'METHLYATION_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.012

Table S272. Gene #45: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 6(2Q32.1) MUTATED	34	31	14
DEL PEAK 6(2Q32.1) WILD-TYPE	214	126	158

Figure S272. Get High-res Image Gene #45: 'del_2q32.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q32.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.03

Table S273. Gene #45: 'del_2q32.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 6(2Q32.1) MUTATED	28	9	25	15	10
DEL PEAK 6(2Q32.1) WILD-TYPE	99	96	204	80	57

Figure S273. Get High-res Image Gene #45: 'del_2q32.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S274. Gene #46: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 7(2Q33.3) MUTATED	31	39	15
DEL PEAK 7(2Q33.3) WILD-TYPE	135	171	234

Figure S274. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q33.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S275. Gene #46: 'del_2q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 7(2Q33.3) MUTATED	29	39	14
DEL PEAK 7(2Q33.3) WILD-TYPE	219	118	158

Figure S275. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q33.3' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00056

Table S276. Gene #46: 'del_2q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 7(2Q33.3) MUTATED	27	32	6
DEL PEAK 7(2Q33.3) WILD-TYPE	207	97	86

Figure S276. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q33.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0018

Table S277. Gene #46: 'del_2q33.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 7(2Q33.3) MUTATED	15	16	3	23	8
DEL PEAK 7(2Q33.3) WILD-TYPE	60	134	22	66	108

Figure S277. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S278. Gene #46: 'del_2q33.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 7(2Q33.3) MUTATED	38	36	10
DEL PEAK 7(2Q33.3) WILD-TYPE	126	292	121

Figure S278. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q33.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00097

Table S279. Gene #46: 'del_2q33.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 7(2Q33.3) MUTATED	22	9	23	25	5
DEL PEAK 7(2Q33.3) WILD-TYPE	105	96	206	70	62

Figure S279. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q33.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0032

Table S280. Gene #46: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 7(2Q33.3) MUTATED	32	19	20
DEL PEAK 7(2Q33.3) WILD-TYPE	112	190	151

Figure S280. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q33.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0031

Table S281. Gene #46: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 7(2Q33.3) MUTATED	6	16	15	9	25
DEL PEAK 7(2Q33.3) WILD-TYPE	41	106	147	92	67

Figure S281. Get High-res Image Gene #46: 'del_2q33.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S282. Gene #47: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 8(2Q37.2) MUTATED	41	63	18
DEL PEAK 8(2Q37.2) WILD-TYPE	125	147	231

Figure S282. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_2q37.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S283. Gene #47: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 8(2Q37.2) MUTATED	39	55	23
DEL PEAK 8(2Q37.2) WILD-TYPE	209	102	149

Figure S283. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_2q37.2' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S284. Gene #47: 'del_2q37.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 8(2Q37.2) MUTATED	42	41	9
DEL PEAK 8(2Q37.2) WILD-TYPE	192	88	83

Figure S284. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_2q37.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S285. Gene #47: 'del_2q37.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 8(2Q37.2) MUTATED	21	22	3	33	13
DEL PEAK 8(2Q37.2) WILD-TYPE	54	128	22	56	103

Figure S285. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S286. Gene #47: 'del_2q37.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 8(2Q37.2) MUTATED	49	57	15
DEL PEAK 8(2Q37.2) WILD-TYPE	115	271	116

Figure S286. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_2q37.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S287. Gene #47: 'del_2q37.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 8(2Q37.2) MUTATED	32	16	32	36	5
DEL PEAK 8(2Q37.2) WILD-TYPE	95	89	197	59	62

Figure S287. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0204 (Fisher's exact test), Q value = 0.027

Table S288. Gene #47: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 8(2Q37.2) MUTATED	41	38	28
DEL PEAK 8(2Q37.2) WILD-TYPE	103	171	143

Figure S288. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_2q37.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S289. Gene #47: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 8(2Q37.2) MUTATED	12	26	21	13	35
DEL PEAK 8(2Q37.2) WILD-TYPE	35	96	141	88	57

Figure S289. Get High-res Image Gene #47: 'del_2q37.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S290. Gene #48: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 9(3P26.2) MUTATED	91	129	30
DEL PEAK 9(3P26.2) WILD-TYPE	75	81	219

Figure S290. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S291. Gene #48: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 9(3P26.2) MUTATED	86	104	45
DEL PEAK 9(3P26.2) WILD-TYPE	162	53	127

Figure S291. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S292. Gene #48: 'del_3p26.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 9(3P26.2) MUTATED	84	82	17
DEL PEAK 9(3P26.2) WILD-TYPE	150	47	75

Figure S292. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S293. Gene #48: 'del_3p26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 9(3P26.2) MUTATED	33	49	12	69	20
DEL PEAK 9(3P26.2) WILD-TYPE	42	101	13	20	96

Figure S293. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S294. Gene #48: 'del_3p26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 9(3P26.2) MUTATED	100	118	31
DEL PEAK 9(3P26.2) WILD-TYPE	64	210	100

Figure S294. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S295. Gene #48: 'del_3p26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 9(3P26.2) MUTATED	64	30	71	74	10
DEL PEAK 9(3P26.2) WILD-TYPE	63	75	158	21	57

Figure S295. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S296. Gene #48: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 9(3P26.2) MUTATED	94	69	54
DEL PEAK 9(3P26.2) WILD-TYPE	50	140	117

Figure S296. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S297. Gene #48: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 9(3P26.2) MUTATED	23	49	45	27	73
DEL PEAK 9(3P26.2) WILD-TYPE	24	73	117	74	19

Figure S297. Get High-res Image Gene #48: 'del_3p26.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S298. Gene #49: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 10(3P14.2) MUTATED	95	142	45
DEL PEAK 10(3P14.2) WILD-TYPE	71	68	204

Figure S298. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S299. Gene #49: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 10(3P14.2) MUTATED	107	117	45
DEL PEAK 10(3P14.2) WILD-TYPE	141	40	127

Figure S299. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S300. Gene #49: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 10(3P14.2) MUTATED	100	93	18
DEL PEAK 10(3P14.2) WILD-TYPE	134	36	74

Figure S300. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S301. Gene #49: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 10(3P14.2) MUTATED	40	58	13	77	23
DEL PEAK 10(3P14.2) WILD-TYPE	35	92	12	12	93

Figure S301. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S302. Gene #49: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 10(3P14.2) MUTATED	112	133	37
DEL PEAK 10(3P14.2) WILD-TYPE	52	195	94

Figure S302. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S303. Gene #49: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 10(3P14.2) MUTATED	69	38	81	83	11
DEL PEAK 10(3P14.2) WILD-TYPE	58	67	148	12	56

Figure S303. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S304. Gene #49: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 10(3P14.2) MUTATED	103	86	58
DEL PEAK 10(3P14.2) WILD-TYPE	41	123	113

Figure S304. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S305. Gene #49: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 10(3P14.2) MUTATED	23	60	55	27	82
DEL PEAK 10(3P14.2) WILD-TYPE	24	62	107	74	10

Figure S305. Get High-res Image Gene #49: 'del_3p14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S306. Gene #50: 'del_3q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 11(3Q11.1) MUTATED	53	33	12
DEL PEAK 11(3Q11.1) WILD-TYPE	113	177	237

Figure S306. Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q11.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S307. Gene #50: 'del_3q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 11(3Q11.1) MUTATED	46	36	10
DEL PEAK 11(3Q11.1) WILD-TYPE	202	121	162

Figure S307. Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S308. Gene #50: 'del_3q11.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 11(3Q11.1) MUTATED	25	18	6	14	8
DEL PEAK 11(3Q11.1) WILD-TYPE	50	132	19	75	108

Figure S308. Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00352 (Fisher's exact test), Q value = 0.0053

Table S309. Gene #50: 'del_3q11.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 11(3Q11.1) MUTATED	33	17	27	16	5
DEL PEAK 11(3Q11.1) WILD-TYPE	94	88	202	79	62

Figure S309. Get High-res Image Gene #50: 'del_3q11.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S310. Gene #51: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 12(3Q26.31) MUTATED	47	7	9
DEL PEAK 12(3Q26.31) WILD-TYPE	119	203	240

Figure S310. Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_3q26.31' versus 'METHLYATION_CNMF'

P value = 0.0082 (Fisher's exact test), Q value = 0.011

Table S311. Gene #51: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 12(3Q26.31) MUTATED	33	18	8
DEL PEAK 12(3Q26.31) WILD-TYPE	215	139	164

Figure S311. Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_3q26.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S312. Gene #51: 'del_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 12(3Q26.31) MUTATED	16	14	5	1	5
DEL PEAK 12(3Q26.31) WILD-TYPE	59	136	20	88	111

Figure S312. Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S313. Gene #51: 'del_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 12(3Q26.31) MUTATED	26	11	21	2	3
DEL PEAK 12(3Q26.31) WILD-TYPE	101	94	208	93	64

Figure S313. Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_3q26.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S314. Gene #51: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 12(3Q26.31) MUTATED	15	16	11	9	2
DEL PEAK 12(3Q26.31) WILD-TYPE	32	106	151	92	90

Figure S314. Get High-res Image Gene #51: 'del_3q26.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S315. Gene #52: 'del_4p16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 13(4P16.3) MUTATED	104	120	47
DEL PEAK 13(4P16.3) WILD-TYPE	62	90	202

Figure S315. Get High-res Image Gene #52: '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 = 2.4e-05

Table S316. Gene #52: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 13(4P16.3) MUTATED	98	95	59
DEL PEAK 13(4P16.3) WILD-TYPE	150	62	113

Figure S316. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 0.00504 (Fisher's exact test), Q value = 0.0073

Table S317. Gene #52: 'del_4p16.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 13(4P16.3) MUTATED	94	72	34
DEL PEAK 13(4P16.3) WILD-TYPE	140	57	58

Figure S317. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S318. Gene #52: 'del_4p16.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 13(4P16.3) MUTATED	46	50	12	52	40
DEL PEAK 13(4P16.3) WILD-TYPE	29	100	13	37	76

Figure S318. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S319. Gene #52: 'del_4p16.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 13(4P16.3) MUTATED	97	127	47
DEL PEAK 13(4P16.3) WILD-TYPE	67	201	84

Figure S319. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S320. Gene #52: 'del_4p16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 13(4P16.3) MUTATED	79	40	72	54	26
DEL PEAK 13(4P16.3) WILD-TYPE	48	65	157	41	41

Figure S320. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S321. Gene #52: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 13(4P16.3) MUTATED	93	73	69
DEL PEAK 13(4P16.3) WILD-TYPE	51	136	102

Figure S321. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S322. Gene #52: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 13(4P16.3) MUTATED	37	54	49	42	53
DEL PEAK 13(4P16.3) WILD-TYPE	10	68	113	59	39

Figure S322. Get High-res Image Gene #52: 'del_4p16.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S323. Gene #53: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 14(4P15.2) MUTATED	98	126	45
DEL PEAK 14(4P15.2) WILD-TYPE	68	84	204

Figure S323. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S324. Gene #53: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 14(4P15.2) MUTATED	94	96	59
DEL PEAK 14(4P15.2) WILD-TYPE	154	61	113

Figure S324. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0033

Table S325. Gene #53: 'del_4p15.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 14(4P15.2) MUTATED	92	73	34
DEL PEAK 14(4P15.2) WILD-TYPE	142	56	58

Figure S325. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S326. Gene #53: 'del_4p15.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 14(4P15.2) MUTATED	45	47	12	54	41
DEL PEAK 14(4P15.2) WILD-TYPE	30	103	13	35	75

Figure S326. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S327. Gene #53: 'del_4p15.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 14(4P15.2) MUTATED	99	125	45
DEL PEAK 14(4P15.2) WILD-TYPE	65	203	86

Figure S327. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S328. Gene #53: 'del_4p15.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 14(4P15.2) MUTATED	81	37	69	55	27
DEL PEAK 14(4P15.2) WILD-TYPE	46	68	160	40	40

Figure S328. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S329. Gene #53: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 14(4P15.2) MUTATED	93	71	65
DEL PEAK 14(4P15.2) WILD-TYPE	51	138	106

Figure S329. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S330. Gene #53: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 14(4P15.2) MUTATED	34	54	47	39	55
DEL PEAK 14(4P15.2) WILD-TYPE	13	68	115	62	37

Figure S330. Get High-res Image Gene #53: 'del_4p15.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S331. Gene #54: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 15(4Q22.1) MUTATED	111	138	49
DEL PEAK 15(4Q22.1) WILD-TYPE	55	72	200

Figure S331. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.0054

Table S332. Gene #54: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 15(4Q22.1) MUTATED	122	89	66
DEL PEAK 15(4Q22.1) WILD-TYPE	126	68	106

Figure S332. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00761 (Fisher's exact test), Q value = 0.011

Table S333. Gene #54: 'del_4q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 15(4Q22.1) MUTATED	122	66	31
DEL PEAK 15(4Q22.1) WILD-TYPE	112	63	61

Figure S333. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S334. Gene #54: 'del_4q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 15(4Q22.1) MUTATED	54	67	13	44	41
DEL PEAK 15(4Q22.1) WILD-TYPE	21	83	12	45	75

Figure S334. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 0.0029 (Fisher's exact test), Q value = 0.0044

Table S335. Gene #54: 'del_4q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 15(4Q22.1) MUTATED	89	162	46
DEL PEAK 15(4Q22.1) WILD-TYPE	75	166	85

Figure S335. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0016

Table S336. Gene #54: 'del_4q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 15(4Q22.1) MUTATED	80	50	96	47	24
DEL PEAK 15(4Q22.1) WILD-TYPE	47	55	133	48	43

Figure S336. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.016

Table S337. Gene #54: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 15(4Q22.1) MUTATED	84	94	73
DEL PEAK 15(4Q22.1) WILD-TYPE	60	115	98

Figure S337. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.036

Table S338. Gene #54: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 15(4Q22.1) MUTATED	28	68	67	41	47
DEL PEAK 15(4Q22.1) WILD-TYPE	19	54	95	60	45

Figure S338. Get High-res Image Gene #54: 'del_4q22.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S339. Gene #55: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 16(4Q34.3) MUTATED	115	136	49
DEL PEAK 16(4Q34.3) WILD-TYPE	51	74	200

Figure S339. Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0031

Table S340. Gene #55: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 16(4Q34.3) MUTATED	122	92	67
DEL PEAK 16(4Q34.3) WILD-TYPE	126	65	105

Figure S340. Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S341. Gene #55: 'del_4q34.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 16(4Q34.3) MUTATED	54	65	12	40	42
DEL PEAK 16(4Q34.3) WILD-TYPE	21	85	13	49	74

Figure S341. Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 0.0199 (Fisher's exact test), Q value = 0.026

Table S342. Gene #55: 'del_4q34.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 16(4Q34.3) MUTATED	89	161	50
DEL PEAK 16(4Q34.3) WILD-TYPE	75	167	81

Figure S342. Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S343. Gene #55: 'del_4q34.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 16(4Q34.3) MUTATED	89	48	98	42	23
DEL PEAK 16(4Q34.3) WILD-TYPE	38	57	131	53	44

Figure S343. Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S344. Gene #55: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 16(4Q34.3) MUTATED	36	73	64	44	42
DEL PEAK 16(4Q34.3) WILD-TYPE	11	49	98	57	50

Figure S344. Get High-res Image Gene #55: 'del_4q34.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S345. Gene #56: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 17(5Q12.1) MUTATED	115	132	35
DEL PEAK 17(5Q12.1) WILD-TYPE	51	78	214

Figure S345. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S346. Gene #56: 'del_5q12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 17(5Q12.1) MUTATED	105	115	48
DEL PEAK 17(5Q12.1) WILD-TYPE	143	42	124

Figure S346. Get High-res Image Gene #56: '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 = 2.4e-05

Table S347. Gene #56: 'del_5q12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 17(5Q12.1) MUTATED	107	77	19
DEL PEAK 17(5Q12.1) WILD-TYPE	127	52	73

Figure S347. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S348. Gene #56: 'del_5q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 17(5Q12.1) MUTATED	53	61	17	50	22
DEL PEAK 17(5Q12.1) WILD-TYPE	22	89	8	39	94

Figure S348. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S349. Gene #56: 'del_5q12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 17(5Q12.1) MUTATED	105	144	32
DEL PEAK 17(5Q12.1) WILD-TYPE	59	184	99

Figure S349. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S350. Gene #56: 'del_5q12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 17(5Q12.1) MUTATED	97	42	78	54	10
DEL PEAK 17(5Q12.1) WILD-TYPE	30	63	151	41	57

Figure S350. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S351. Gene #56: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 17(5Q12.1) MUTATED	95	95	60
DEL PEAK 17(5Q12.1) WILD-TYPE	49	114	111

Figure S351. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S352. Gene #56: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 17(5Q12.1) MUTATED	38	64	63	31	54
DEL PEAK 17(5Q12.1) WILD-TYPE	9	58	99	70	38

Figure S352. Get High-res Image Gene #56: 'del_5q12.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S353. Gene #57: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 18(6P25.3) MUTATED	67	89	32
DEL PEAK 18(6P25.3) WILD-TYPE	99	121	217

Figure S353. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S354. Gene #57: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 18(6P25.3) MUTATED	81	65	35
DEL PEAK 18(6P25.3) WILD-TYPE	167	92	137

Figure S354. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0021

Table S355. Gene #57: 'del_6p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 18(6P25.3) MUTATED	68	48	14
DEL PEAK 18(6P25.3) WILD-TYPE	166	81	78

Figure S355. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S356. Gene #57: 'del_6p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 18(6P25.3) MUTATED	30	41	10	32	17
DEL PEAK 18(6P25.3) WILD-TYPE	45	109	15	57	99

Figure S356. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S357. Gene #57: 'del_6p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 18(6P25.3) MUTATED	59	107	21
DEL PEAK 18(6P25.3) WILD-TYPE	105	221	110

Figure S357. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S358. Gene #57: 'del_6p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 18(6P25.3) MUTATED	53	30	64	33	7
DEL PEAK 18(6P25.3) WILD-TYPE	74	75	165	62	60

Figure S358. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.048

Table S359. Gene #57: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 18(6P25.3) MUTATED	54	69	42
DEL PEAK 18(6P25.3) WILD-TYPE	90	140	129

Figure S359. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00056

Table S360. Gene #57: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 18(6P25.3) MUTATED	14	57	39	23	32
DEL PEAK 18(6P25.3) WILD-TYPE	33	65	123	78	60

Figure S360. Get High-res Image Gene #57: 'del_6p25.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S361. Gene #58: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 19(6Q16.3) MUTATED	41	83	23
DEL PEAK 19(6Q16.3) WILD-TYPE	125	127	226

Figure S361. Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q16.3' versus 'METHLYATION_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.034

Table S362. Gene #58: 'del_6q16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 19(6Q16.3) MUTATED	53	50	35
DEL PEAK 19(6Q16.3) WILD-TYPE	195	107	137

Figure S362. Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q16.3' versus 'MRNASEQ_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.012

Table S363. Gene #58: 'del_6q16.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 19(6Q16.3) MUTATED	54	41	13
DEL PEAK 19(6Q16.3) WILD-TYPE	180	88	79

Figure S363. Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_6q16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00865 (Fisher's exact test), Q value = 0.012

Table S364. Gene #58: 'del_6q16.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 19(6Q16.3) MUTATED	21	35	5	31	16
DEL PEAK 19(6Q16.3) WILD-TYPE	54	115	20	58	100

Figure S364. Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00829 (Fisher's exact test), Q value = 0.011

Table S365. Gene #58: 'del_6q16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 19(6Q16.3) MUTATED	34	25	49	32	7
DEL PEAK 19(6Q16.3) WILD-TYPE	93	80	180	63	60

Figure S365. Get High-res Image Gene #58: 'del_6q16.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S366. Gene #59: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 20(6Q26) MUTATED	46	80	26
DEL PEAK 20(6Q26) WILD-TYPE	120	130	223

Figure S366. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.0236 (Fisher's exact test), Q value = 0.03

Table S367. Gene #59: 'del_6q26' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 20(6Q26) MUTATED	54	40	14
DEL PEAK 20(6Q26) WILD-TYPE	180	89	78

Figure S367. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0486 (Fisher's exact test), Q value = 0.059

Table S368. Gene #59: 'del_6q26' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 20(6Q26) MUTATED	24	32	4	28	20
DEL PEAK 20(6Q26) WILD-TYPE	51	118	21	61	96

Figure S368. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.015

Table S369. Gene #59: 'del_6q26' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 20(6Q26) MUTATED	49	83	20
DEL PEAK 20(6Q26) WILD-TYPE	115	245	111

Figure S369. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.051

Table S370. Gene #59: 'del_6q26' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 20(6Q26) MUTATED	35	27	52	30	8
DEL PEAK 20(6Q26) WILD-TYPE	92	78	177	65	59

Figure S370. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.034

Table S371. Gene #59: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 20(6Q26) MUTATED	46	46	33
DEL PEAK 20(6Q26) WILD-TYPE	98	163	138

Figure S371. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.047

Table S372. Gene #59: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 20(6Q26) MUTATED	11	23	46	16	29
DEL PEAK 20(6Q26) WILD-TYPE	36	99	116	85	63

Figure S372. Get High-res Image Gene #59: 'del_6q26' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S373. Gene #60: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 21(7Q31.1) MUTATED	44	65	18
DEL PEAK 21(7Q31.1) WILD-TYPE	122	145	231

Figure S373. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 0.00479 (Fisher's exact test), Q value = 0.0069

Table S374. Gene #60: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 21(7Q31.1) MUTATED	55	42	22
DEL PEAK 21(7Q31.1) WILD-TYPE	193	115	150

Figure S374. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0056

Table S375. Gene #60: 'del_7q31.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 21(7Q31.1) MUTATED	54	35	9
DEL PEAK 21(7Q31.1) WILD-TYPE	180	94	83

Figure S375. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00763 (Fisher's exact test), Q value = 0.011

Table S376. Gene #60: 'del_7q31.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 21(7Q31.1) MUTATED	22	31	7	25	13
DEL PEAK 21(7Q31.1) WILD-TYPE	53	119	18	64	103

Figure S376. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.011

Table S377. Gene #60: 'del_7q31.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 21(7Q31.1) MUTATED	46	62	18
DEL PEAK 21(7Q31.1) WILD-TYPE	118	266	113

Figure S377. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.0096

Table S378. Gene #60: 'del_7q31.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 21(7Q31.1) MUTATED	38	19	37	24	8
DEL PEAK 21(7Q31.1) WILD-TYPE	89	86	192	71	59

Figure S378. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.022

Table S379. Gene #60: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 21(7Q31.1) MUTATED	12	36	27	14	24
DEL PEAK 21(7Q31.1) WILD-TYPE	35	86	135	87	68

Figure S379. Get High-res Image Gene #60: 'del_7q31.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S380. Gene #61: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 22(7Q36.3) MUTATED	60	86	17
DEL PEAK 22(7Q36.3) WILD-TYPE	106	124	232

Figure S380. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_7q36.3' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S381. Gene #61: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 22(7Q36.3) MUTATED	57	63	35
DEL PEAK 22(7Q36.3) WILD-TYPE	191	94	137

Figure S381. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.003

Table S382. Gene #61: 'del_7q36.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 22(7Q36.3) MUTATED	61	45	13
DEL PEAK 22(7Q36.3) WILD-TYPE	173	84	79

Figure S382. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S383. Gene #61: 'del_7q36.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 22(7Q36.3) MUTATED	31	36	5	31	16
DEL PEAK 22(7Q36.3) WILD-TYPE	44	114	20	58	100

Figure S383. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S384. Gene #61: 'del_7q36.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 22(7Q36.3) MUTATED	65	77	21
DEL PEAK 22(7Q36.3) WILD-TYPE	99	251	110

Figure S384. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S385. Gene #61: 'del_7q36.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 22(7Q36.3) MUTATED	52	23	46	34	8
DEL PEAK 22(7Q36.3) WILD-TYPE	75	82	183	61	59

Figure S385. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00061

Table S386. Gene #61: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 22(7Q36.3) MUTATED	58	55	35
DEL PEAK 22(7Q36.3) WILD-TYPE	86	154	136

Figure S386. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0126 (Fisher's exact test), Q value = 0.017

Table S387. Gene #61: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 22(7Q36.3) MUTATED	16	41	41	17	33
DEL PEAK 22(7Q36.3) WILD-TYPE	31	81	121	84	59

Figure S387. Get High-res Image Gene #61: 'del_7q36.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S388. Gene #62: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 23(8P23.2) MUTATED	77	109	26
DEL PEAK 23(8P23.2) WILD-TYPE	89	101	223

Figure S388. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S389. Gene #62: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 23(8P23.2) MUTATED	72	87	41
DEL PEAK 23(8P23.2) WILD-TYPE	176	70	131

Figure S389. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S390. Gene #62: 'del_8p23.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 23(8P23.2) MUTATED	62	69	25
DEL PEAK 23(8P23.2) WILD-TYPE	172	60	67

Figure S390. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S391. Gene #62: 'del_8p23.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 23(8P23.2) MUTATED	45	33	8	51	19
DEL PEAK 23(8P23.2) WILD-TYPE	30	117	17	38	97

Figure S391. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S392. Gene #62: 'del_8p23.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 23(8P23.2) MUTATED	84	99	28
DEL PEAK 23(8P23.2) WILD-TYPE	80	229	103

Figure S392. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S393. Gene #62: 'del_8p23.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 23(8P23.2) MUTATED	61	28	54	56	12
DEL PEAK 23(8P23.2) WILD-TYPE	66	77	175	39	55

Figure S393. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S394. Gene #62: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 23(8P23.2) MUTATED	76	64	44
DEL PEAK 23(8P23.2) WILD-TYPE	68	145	127

Figure S394. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S395. Gene #62: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 23(8P23.2) MUTATED	26	39	48	19	52
DEL PEAK 23(8P23.2) WILD-TYPE	21	83	114	82	40

Figure S395. Get High-res Image Gene #62: 'del_8p23.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S396. Gene #63: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 24(9P23) MUTATED	113	135	54
DEL PEAK 24(9P23) WILD-TYPE	53	75	195

Figure S396. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0022

Table S397. Gene #63: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 24(9P23) MUTATED	118	95	70
DEL PEAK 24(9P23) WILD-TYPE	130	62	102

Figure S397. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.021

Table S398. Gene #63: 'del_9p23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 24(9P23) MUTATED	117	66	31
DEL PEAK 24(9P23) WILD-TYPE	117	63	61

Figure S398. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00509 (Fisher's exact test), Q value = 0.0073

Table S399. Gene #63: 'del_9p23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 24(9P23) MUTATED	45	67	11	50	41
DEL PEAK 24(9P23) WILD-TYPE	30	83	14	39	75

Figure S399. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0018

Table S400. Gene #63: 'del_9p23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 24(9P23) MUTATED	94	160	47
DEL PEAK 24(9P23) WILD-TYPE	70	168	84

Figure S400. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S401. Gene #63: 'del_9p23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 24(9P23) MUTATED	82	43	98	54	24
DEL PEAK 24(9P23) WILD-TYPE	45	62	131	41	43

Figure S401. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.043 (Fisher's exact test), Q value = 0.053

Table S402. Gene #63: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 24(9P23) MUTATED	84	99	77
DEL PEAK 24(9P23) WILD-TYPE	60	110	94

Figure S402. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.039

Table S403. Gene #63: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 24(9P23) MUTATED	28	65	72	41	54
DEL PEAK 24(9P23) WILD-TYPE	19	57	90	60	38

Figure S403. Get High-res Image Gene #63: 'del_9p23' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S404. Gene #64: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 25(9P21.3) MUTATED	114	164	56
DEL PEAK 25(9P21.3) WILD-TYPE	52	46	193

Figure S404. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S405. Gene #64: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 25(9P21.3) MUTATED	121	120	75
DEL PEAK 25(9P21.3) WILD-TYPE	127	37	97

Figure S405. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S406. Gene #64: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 25(9P21.3) MUTATED	120	97	31
DEL PEAK 25(9P21.3) WILD-TYPE	114	32	61

Figure S406. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S407. Gene #64: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 25(9P21.3) MUTATED	49	70	15	77	37
DEL PEAK 25(9P21.3) WILD-TYPE	26	80	10	12	79

Figure S407. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S408. Gene #64: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 25(9P21.3) MUTATED	124	158	51
DEL PEAK 25(9P21.3) WILD-TYPE	40	170	80

Figure S408. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S409. Gene #64: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 25(9P21.3) MUTATED	85	43	102	80	23
DEL PEAK 25(9P21.3) WILD-TYPE	42	62	127	15	44

Figure S409. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S410. Gene #64: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 25(9P21.3) MUTATED	109	99	86
DEL PEAK 25(9P21.3) WILD-TYPE	35	110	85

Figure S410. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S411. Gene #64: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 25(9P21.3) MUTATED	32	70	68	44	80
DEL PEAK 25(9P21.3) WILD-TYPE	15	52	94	57	12

Figure S411. Get High-res Image Gene #64: 'del_9p21.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S412. Gene #65: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 26(9Q21.11) MUTATED	68	83	25
DEL PEAK 26(9Q21.11) WILD-TYPE	98	127	224

Figure S412. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S413. Gene #65: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 26(9Q21.11) MUTATED	58	67	42
DEL PEAK 26(9Q21.11) WILD-TYPE	190	90	130

Figure S413. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.027

Table S414. Gene #65: 'del_9q21.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 26(9Q21.11) MUTATED	67	44	16
DEL PEAK 26(9Q21.11) WILD-TYPE	167	85	76

Figure S414. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S415. Gene #65: 'del_9q21.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 26(9Q21.11) MUTATED	32	35	4	35	21
DEL PEAK 26(9Q21.11) WILD-TYPE	43	115	21	54	95

Figure S415. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S416. Gene #65: 'del_9q21.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 26(9Q21.11) MUTATED	68	79	29
DEL PEAK 26(9Q21.11) WILD-TYPE	96	249	102

Figure S416. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S417. Gene #65: 'del_9q21.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 26(9Q21.11) MUTATED	61	19	45	36	15
DEL PEAK 26(9Q21.11) WILD-TYPE	66	86	184	59	52

Figure S417. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00105 (Fisher's exact test), Q value = 0.0018

Table S418. Gene #65: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 26(9Q21.11) MUTATED	58	46	50
DEL PEAK 26(9Q21.11) WILD-TYPE	86	163	121

Figure S418. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00568 (Fisher's exact test), Q value = 0.0081

Table S419. Gene #65: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 26(9Q21.11) MUTATED	22	31	38	27	36
DEL PEAK 26(9Q21.11) WILD-TYPE	25	91	124	74	56

Figure S419. Get High-res Image Gene #65: 'del_9q21.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S420. Gene #66: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 27(10P15.3) MUTATED	39	74	18
DEL PEAK 27(10P15.3) WILD-TYPE	127	136	231

Figure S420. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0033

Table S421. Gene #66: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 27(10P15.3) MUTATED	42	49	31
DEL PEAK 27(10P15.3) WILD-TYPE	206	108	141

Figure S421. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S422. Gene #66: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 27(10P15.3) MUTATED	36	45	14
DEL PEAK 27(10P15.3) WILD-TYPE	198	84	78

Figure S422. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S423. Gene #66: 'del_10p15.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 27(10P15.3) MUTATED	15	24	7	35	14
DEL PEAK 27(10P15.3) WILD-TYPE	60	126	18	54	102

Figure S423. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 0.00235 (Fisher's exact test), Q value = 0.0036

Table S424. Gene #66: 'del_10p15.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 27(10P15.3) MUTATED	50	61	20
DEL PEAK 27(10P15.3) WILD-TYPE	114	267	111

Figure S424. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S425. Gene #66: 'del_10p15.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 27(10P15.3) MUTATED	30	20	39	36	6
DEL PEAK 27(10P15.3) WILD-TYPE	97	85	190	59	61

Figure S425. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0069 (Fisher's exact test), Q value = 0.0098

Table S426. Gene #66: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 27(10P15.3) MUTATED	44	40	28
DEL PEAK 27(10P15.3) WILD-TYPE	100	169	143

Figure S426. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S427. Gene #66: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 27(10P15.3) MUTATED	14	24	22	16	36
DEL PEAK 27(10P15.3) WILD-TYPE	33	98	140	85	56

Figure S427. Get High-res Image Gene #66: 'del_10p15.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S428. Gene #67: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 28(10P11.21) MUTATED	25	67	10
DEL PEAK 28(10P11.21) WILD-TYPE	141	143	239

Figure S428. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S429. Gene #67: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 28(10P11.21) MUTATED	23	53	21
DEL PEAK 28(10P11.21) WILD-TYPE	225	104	151

Figure S429. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S430. Gene #67: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 28(10P11.21) MUTATED	24	45	9
DEL PEAK 28(10P11.21) WILD-TYPE	210	84	83

Figure S430. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S431. Gene #67: 'del_10p11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 28(10P11.21) MUTATED	11	16	4	39	8
DEL PEAK 28(10P11.21) WILD-TYPE	64	134	21	50	108

Figure S431. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S432. Gene #67: 'del_10p11.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 28(10P11.21) MUTATED	49	40	12
DEL PEAK 28(10P11.21) WILD-TYPE	115	288	119

Figure S432. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S433. Gene #67: 'del_10p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 28(10P11.21) MUTATED	24	9	25	41	2
DEL PEAK 28(10P11.21) WILD-TYPE	103	96	204	54	65

Figure S433. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S434. Gene #67: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 28(10P11.21) MUTATED	42	26	21
DEL PEAK 28(10P11.21) WILD-TYPE	102	183	150

Figure S434. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S435. Gene #67: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 28(10P11.21) MUTATED	9	13	16	11	40
DEL PEAK 28(10P11.21) WILD-TYPE	38	109	146	90	52

Figure S435. Get High-res Image Gene #67: 'del_10p11.21' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S436. Gene #68: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 29(10Q21.1) MUTATED	39	57	16
DEL PEAK 29(10Q21.1) WILD-TYPE	127	153	233

Figure S436. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S437. Gene #68: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 29(10Q21.1) MUTATED	28	54	22
DEL PEAK 29(10Q21.1) WILD-TYPE	220	103	150

Figure S437. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q21.1' versus 'MRNASEQ_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.0035

Table S438. Gene #68: 'del_10q21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 29(10Q21.1) MUTATED	36	36	10
DEL PEAK 29(10Q21.1) WILD-TYPE	198	93	82

Figure S438. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S439. Gene #68: 'del_10q21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 29(10Q21.1) MUTATED	13	24	5	31	9
DEL PEAK 29(10Q21.1) WILD-TYPE	62	126	20	58	107

Figure S439. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0019

Table S440. Gene #68: 'del_10q21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 29(10Q21.1) MUTATED	43	56	13
DEL PEAK 29(10Q21.1) WILD-TYPE	121	272	118

Figure S440. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S441. Gene #68: 'del_10q21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 29(10Q21.1) MUTATED	37	13	29	31	2
DEL PEAK 29(10Q21.1) WILD-TYPE	90	92	200	64	65

Figure S441. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00652 (Fisher's exact test), Q value = 0.0093

Table S442. Gene #68: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 29(10Q21.1) MUTATED	39	32	24
DEL PEAK 29(10Q21.1) WILD-TYPE	105	177	147

Figure S442. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S443. Gene #68: 'del_10q21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 29(10Q21.1) MUTATED	12	22	14	16	31
DEL PEAK 29(10Q21.1) WILD-TYPE	35	100	148	85	61

Figure S443. Get High-res Image Gene #68: 'del_10q21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S444. Gene #69: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 30(10Q22.3) MUTATED	54	65	16
DEL PEAK 30(10Q22.3) WILD-TYPE	112	145	233

Figure S444. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S445. Gene #69: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 30(10Q22.3) MUTATED	45	58	23
DEL PEAK 30(10Q22.3) WILD-TYPE	203	99	149

Figure S445. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q22.3' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S446. Gene #69: 'del_10q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 30(10Q22.3) MUTATED	45	43	9
DEL PEAK 30(10Q22.3) WILD-TYPE	189	86	83

Figure S446. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S447. Gene #69: 'del_10q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 30(10Q22.3) MUTATED	19	27	6	36	9
DEL PEAK 30(10Q22.3) WILD-TYPE	56	123	19	53	107

Figure S447. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S448. Gene #69: 'del_10q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 30(10Q22.3) MUTATED	51	71	13
DEL PEAK 30(10Q22.3) WILD-TYPE	113	257	118

Figure S448. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S449. Gene #69: 'del_10q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 30(10Q22.3) MUTATED	41	21	34	36	3
DEL PEAK 30(10Q22.3) WILD-TYPE	86	84	195	59	64

Figure S449. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S450. Gene #69: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 30(10Q22.3) MUTATED	49	39	24
DEL PEAK 30(10Q22.3) WILD-TYPE	95	170	147

Figure S450. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S451. Gene #69: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 30(10Q22.3) MUTATED	15	30	17	14	36
DEL PEAK 30(10Q22.3) WILD-TYPE	32	92	145	87	56

Figure S451. Get High-res Image Gene #69: 'del_10q22.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S452. Gene #70: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 31(10Q23.31) MUTATED	69	91	23
DEL PEAK 31(10Q23.31) WILD-TYPE	97	119	226

Figure S452. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S453. Gene #70: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 31(10Q23.31) MUTATED	59	73	37
DEL PEAK 31(10Q23.31) WILD-TYPE	189	84	135

Figure S453. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S454. Gene #70: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 31(10Q23.31) MUTATED	67	49	12
DEL PEAK 31(10Q23.31) WILD-TYPE	167	80	80

Figure S454. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S455. Gene #70: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 31(10Q23.31) MUTATED	26	44	6	39	13
DEL PEAK 31(10Q23.31) WILD-TYPE	49	106	19	50	103

Figure S455. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S456. Gene #70: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 31(10Q23.31) MUTATED	62	103	18
DEL PEAK 31(10Q23.31) WILD-TYPE	102	225	113

Figure S456. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S457. Gene #70: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 31(10Q23.31) MUTATED	57	27	53	40	6
DEL PEAK 31(10Q23.31) WILD-TYPE	70	78	176	55	61

Figure S457. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00088

Table S458. Gene #70: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 31(10Q23.31) MUTATED	60	58	37
DEL PEAK 31(10Q23.31) WILD-TYPE	84	151	134

Figure S458. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S459. Gene #70: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 31(10Q23.31) MUTATED	21	41	32	21	40
DEL PEAK 31(10Q23.31) WILD-TYPE	26	81	130	80	52

Figure S459. Get High-res Image Gene #70: 'del_10q23.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S460. Gene #71: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 32(11P15.5) MUTATED	61	95	19
DEL PEAK 32(11P15.5) WILD-TYPE	105	115	230

Figure S460. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #1: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S461. Gene #71: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 32(11P15.5) MUTATED	62	71	28
DEL PEAK 32(11P15.5) WILD-TYPE	186	86	144

Figure S461. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S462. Gene #71: 'del_11p15.5' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 32(11P15.5) MUTATED	53	59	13
DEL PEAK 32(11P15.5) WILD-TYPE	181	70	79

Figure S462. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S463. Gene #71: 'del_11p15.5' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 32(11P15.5) MUTATED	25	33	9	42	16
DEL PEAK 32(11P15.5) WILD-TYPE	50	117	16	47	100

Figure S463. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S464. Gene #71: 'del_11p15.5' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 32(11P15.5) MUTATED	68	80	27
DEL PEAK 32(11P15.5) WILD-TYPE	96	248	104

Figure S464. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S465. Gene #71: 'del_11p15.5' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 32(11P15.5) MUTATED	46	22	54	43	10
DEL PEAK 32(11P15.5) WILD-TYPE	81	83	175	52	57

Figure S465. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

Table S466. Gene #71: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 32(11P15.5) MUTATED	60	48	40
DEL PEAK 32(11P15.5) WILD-TYPE	84	161	131

Figure S466. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.00094

Table S467. Gene #71: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 32(11P15.5) MUTATED	14	36	36	20	42
DEL PEAK 32(11P15.5) WILD-TYPE	33	86	126	81	50

Figure S467. Get High-res Image Gene #71: 'del_11p15.5' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S468. Gene #72: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 33(11Q25) MUTATED	58	101	19
DEL PEAK 33(11Q25) WILD-TYPE	108	109	230

Figure S468. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S469. Gene #72: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 33(11Q25) MUTATED	63	77	30
DEL PEAK 33(11Q25) WILD-TYPE	185	80	142

Figure S469. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S470. Gene #72: 'del_11q25' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 33(11Q25) MUTATED	56	58	18
DEL PEAK 33(11Q25) WILD-TYPE	178	71	74

Figure S470. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S471. Gene #72: 'del_11q25' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 33(11Q25) MUTATED	25	38	7	47	15
DEL PEAK 33(11Q25) WILD-TYPE	50	112	18	42	101

Figure S471. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S472. Gene #72: 'del_11q25' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 33(11Q25) MUTATED	74	79	24
DEL PEAK 33(11Q25) WILD-TYPE	90	249	107

Figure S472. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S473. Gene #72: 'del_11q25' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 33(11Q25) MUTATED	39	23	55	51	9
DEL PEAK 33(11Q25) WILD-TYPE	88	82	174	44	58

Figure S473. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S474. Gene #72: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 33(11Q25) MUTATED	66	53	37
DEL PEAK 33(11Q25) WILD-TYPE	78	156	134

Figure S474. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S475. Gene #72: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 33(11Q25) MUTATED	12	37	39	18	50
DEL PEAK 33(11Q25) WILD-TYPE	35	85	123	83	42

Figure S475. Get High-res Image Gene #72: 'del_11q25' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S476. Gene #73: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 34(12P13.1) MUTATED	64	32	17
DEL PEAK 34(12P13.1) WILD-TYPE	102	178	232

Figure S476. Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12p13.1' versus 'METHLYATION_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.052

Table S477. Gene #73: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 34(12P13.1) MUTATED	50	34	21
DEL PEAK 34(12P13.1) WILD-TYPE	198	123	151

Figure S477. Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S478. Gene #73: 'del_12p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 34(12P13.1) MUTATED	30	19	10	7	11
DEL PEAK 34(12P13.1) WILD-TYPE	45	131	15	82	105

Figure S478. Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S479. Gene #73: 'del_12p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 34(12P13.1) MUTATED	45	16	38	7	7
DEL PEAK 34(12P13.1) WILD-TYPE	82	89	191	88	60

Figure S479. Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_12p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S480. Gene #73: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 34(12P13.1) MUTATED	20	25	30	19	7
DEL PEAK 34(12P13.1) WILD-TYPE	27	97	132	82	85

Figure S480. Get High-res Image Gene #73: 'del_12p13.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S481. Gene #74: 'del_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 35(12Q23.1) MUTATED	51	51	7
DEL PEAK 35(12Q23.1) WILD-TYPE	115	159	242

Figure S481. Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.0043

Table S482. Gene #74: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 35(12Q23.1) MUTATED	42	41	20
DEL PEAK 35(12Q23.1) WILD-TYPE	206	116	152

Figure S482. Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.021

Table S483. Gene #74: 'del_12q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 35(12Q23.1) MUTATED	40	30	8
DEL PEAK 35(12Q23.1) WILD-TYPE	194	99	84

Figure S483. Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S484. Gene #74: 'del_12q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 35(12Q23.1) MUTATED	19	24	9	19	7
DEL PEAK 35(12Q23.1) WILD-TYPE	56	126	16	70	109

Figure S484. Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.013

Table S485. Gene #74: 'del_12q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 35(12Q23.1) MUTATED	33	13	39	19	5
DEL PEAK 35(12Q23.1) WILD-TYPE	94	92	190	76	62

Figure S485. Get High-res Image Gene #74: 'del_12q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S486. Gene #75: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 36(13Q12.11) MUTATED	20	101	17
DEL PEAK 36(13Q12.11) WILD-TYPE	146	109	232

Figure S486. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S487. Gene #75: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 36(13Q12.11) MUTATED	49	60	22
DEL PEAK 36(13Q12.11) WILD-TYPE	199	97	150

Figure S487. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S488. Gene #75: 'del_13q12.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 36(13Q12.11) MUTATED	40	56	17
DEL PEAK 36(13Q12.11) WILD-TYPE	194	73	75

Figure S488. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S489. Gene #75: 'del_13q12.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 36(13Q12.11) MUTATED	26	23	4	45	15
DEL PEAK 36(13Q12.11) WILD-TYPE	49	127	21	44	101

Figure S489. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S490. Gene #75: 'del_13q12.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 36(13Q12.11) MUTATED	67	50	21
DEL PEAK 36(13Q12.11) WILD-TYPE	97	278	110

Figure S490. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q12.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S491. Gene #75: 'del_13q12.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 36(13Q12.11) MUTATED	28	17	35	50	8
DEL PEAK 36(13Q12.11) WILD-TYPE	99	88	194	45	59

Figure S491. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q12.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S492. Gene #75: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 36(13Q12.11) MUTATED	57	35	31
DEL PEAK 36(13Q12.11) WILD-TYPE	87	174	140

Figure S492. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S493. Gene #75: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 36(13Q12.11) MUTATED	8	27	25	14	49
DEL PEAK 36(13Q12.11) WILD-TYPE	39	95	137	87	43

Figure S493. Get High-res Image Gene #75: 'del_13q12.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S494. Gene #76: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 37(13Q14.2) MUTATED	9	99	17
DEL PEAK 37(13Q14.2) WILD-TYPE	157	111	232

Figure S494. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S495. Gene #76: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 37(13Q14.2) MUTATED	41	55	21
DEL PEAK 37(13Q14.2) WILD-TYPE	207	102	151

Figure S495. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S496. Gene #76: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 37(13Q14.2) MUTATED	36	56	18
DEL PEAK 37(13Q14.2) WILD-TYPE	198	73	74

Figure S496. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S497. Gene #76: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 37(13Q14.2) MUTATED	26	21	5	43	15
DEL PEAK 37(13Q14.2) WILD-TYPE	49	129	20	46	101

Figure S497. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S498. Gene #76: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 37(13Q14.2) MUTATED	62	45	17
DEL PEAK 37(13Q14.2) WILD-TYPE	102	283	114

Figure S498. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S499. Gene #76: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 37(13Q14.2) MUTATED	24	15	31	48	6
DEL PEAK 37(13Q14.2) WILD-TYPE	103	90	198	47	61

Figure S499. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S500. Gene #76: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 37(13Q14.2) MUTATED	53	29	25
DEL PEAK 37(13Q14.2) WILD-TYPE	91	180	146

Figure S500. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S501. Gene #76: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 37(13Q14.2) MUTATED	8	21	21	11	46
DEL PEAK 37(13Q14.2) WILD-TYPE	39	101	141	90	46

Figure S501. Get High-res Image Gene #76: 'del_13q14.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S502. Gene #77: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 38(13Q21.31) MUTATED	8	98	20
DEL PEAK 38(13Q21.31) WILD-TYPE	158	112	229

Figure S502. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S503. Gene #77: 'del_13q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 38(13Q21.31) MUTATED	43	52	22
DEL PEAK 38(13Q21.31) WILD-TYPE	205	105	150

Figure S503. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_13q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S504. Gene #77: 'del_13q21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 38(13Q21.31) MUTATED	40	52	16
DEL PEAK 38(13Q21.31) WILD-TYPE	194	77	76

Figure S504. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_13q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S505. Gene #77: 'del_13q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 38(13Q21.31) MUTATED	21	26	7	40	14
DEL PEAK 38(13Q21.31) WILD-TYPE	54	124	18	49	102

Figure S505. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_13q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S506. Gene #77: 'del_13q21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 38(13Q21.31) MUTATED	57	52	17
DEL PEAK 38(13Q21.31) WILD-TYPE	107	276	114

Figure S506. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_13q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S507. Gene #77: 'del_13q21.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 38(13Q21.31) MUTATED	25	14	37	44	6
DEL PEAK 38(13Q21.31) WILD-TYPE	102	91	192	51	61

Figure S507. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_13q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S508. Gene #77: 'del_13q21.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 38(13Q21.31) MUTATED	49	33	27
DEL PEAK 38(13Q21.31) WILD-TYPE	95	176	144

Figure S508. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_13q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S509. Gene #77: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 38(13Q21.31) MUTATED	6	28	19	13	43
DEL PEAK 38(13Q21.31) WILD-TYPE	41	94	143	88	49

Figure S509. Get High-res Image Gene #77: 'del_13q21.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q23.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S510. Gene #78: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 39(14Q23.3) MUTATED	80	74	33
DEL PEAK 39(14Q23.3) WILD-TYPE	86	136	216

Figure S510. Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'METHLYATION_CNMF'

P value = 0.00272 (Fisher's exact test), Q value = 0.0042

Table S511. Gene #78: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 39(14Q23.3) MUTATED	74	62	38
DEL PEAK 39(14Q23.3) WILD-TYPE	174	95	134

Figure S511. Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S512. Gene #78: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 39(14Q23.3) MUTATED	40	40	7	16	25
DEL PEAK 39(14Q23.3) WILD-TYPE	35	110	18	73	91

Figure S512. Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S513. Gene #78: 'del_14q23.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 39(14Q23.3) MUTATED	69	28	57	19	14
DEL PEAK 39(14Q23.3) WILD-TYPE	58	77	172	76	53

Figure S513. Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_14q23.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S514. Gene #78: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 39(14Q23.3) MUTATED	27	44	45	22	19
DEL PEAK 39(14Q23.3) WILD-TYPE	20	78	117	79	73

Figure S514. Get High-res Image Gene #78: 'del_14q23.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q32.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S515. Gene #79: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 40(14Q32.32) MUTATED	74	81	35
DEL PEAK 40(14Q32.32) WILD-TYPE	92	129	214

Figure S515. Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.32' versus 'METHLYATION_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.03

Table S516. Gene #79: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 40(14Q32.32) MUTATED	78	58	40
DEL PEAK 40(14Q32.32) WILD-TYPE	170	99	132

Figure S516. Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_14q32.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00168 (Fisher's exact test), Q value = 0.0027

Table S517. Gene #79: 'del_14q32.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 40(14Q32.32) MUTATED	37	42	9	20	28
DEL PEAK 40(14Q32.32) WILD-TYPE	38	108	16	69	88

Figure S517. Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00215 (Fisher's exact test), Q value = 0.0034

Table S518. Gene #79: 'del_14q32.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 40(14Q32.32) MUTATED	58	27	64	24	17
DEL PEAK 40(14Q32.32) WILD-TYPE	69	78	165	71	50

Figure S518. Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_14q32.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.018

Table S519. Gene #79: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 40(14Q32.32) MUTATED	24	42	45	25	24
DEL PEAK 40(14Q32.32) WILD-TYPE	23	80	117	76	68

Figure S519. Get High-res Image Gene #79: 'del_14q32.32' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S520. Gene #80: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 41(15Q11.2) MUTATED	72	85	26
DEL PEAK 41(15Q11.2) WILD-TYPE	94	125	223

Figure S520. Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00182 (Fisher's exact test), Q value = 0.0029

Table S521. Gene #80: 'del_15q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 41(15Q11.2) MUTATED	77	39	13
DEL PEAK 41(15Q11.2) WILD-TYPE	157	90	79

Figure S521. Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_15q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00128 (Fisher's exact test), Q value = 0.0021

Table S522. Gene #80: 'del_15q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 41(15Q11.2) MUTATED	32	45	8	26	18
DEL PEAK 41(15Q11.2) WILD-TYPE	43	105	17	63	98

Figure S522. Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.03

Table S523. Gene #80: 'del_15q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 41(15Q11.2) MUTATED	52	105	26
DEL PEAK 41(15Q11.2) WILD-TYPE	112	223	105

Figure S523. Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_15q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S524. Gene #80: 'del_15q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 41(15Q11.2) MUTATED	60	26	59	29	9
DEL PEAK 41(15Q11.2) WILD-TYPE	67	79	170	66	58

Figure S524. Get High-res Image Gene #80: 'del_15q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S525. Gene #81: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 42(16P13.3) MUTATED	87	67	24
DEL PEAK 42(16P13.3) WILD-TYPE	79	143	225

Figure S525. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00438 (Fisher's exact test), Q value = 0.0064

Table S526. Gene #81: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 42(16P13.3) MUTATED	75	57	35
DEL PEAK 42(16P13.3) WILD-TYPE	173	100	137

Figure S526. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S527. Gene #81: 'del_16p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 42(16P13.3) MUTATED	40	34	12	16	16
DEL PEAK 42(16P13.3) WILD-TYPE	35	116	13	73	100

Figure S527. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.0037

Table S528. Gene #81: 'del_16p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 42(16P13.3) MUTATED	60	93	24
DEL PEAK 42(16P13.3) WILD-TYPE	104	235	107

Figure S528. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S529. Gene #81: 'del_16p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 42(16P13.3) MUTATED	65	28	58	18	8
DEL PEAK 42(16P13.3) WILD-TYPE	62	77	171	77	59

Figure S529. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0037

Table S530. Gene #81: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 42(16P13.3) MUTATED	57	60	37
DEL PEAK 42(16P13.3) WILD-TYPE	87	149	134

Figure S530. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S531. Gene #81: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 42(16P13.3) MUTATED	32	45	39	20	18
DEL PEAK 42(16P13.3) WILD-TYPE	15	77	123	81	74

Figure S531. Get High-res Image Gene #81: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S532. Gene #82: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 43(16P13.3) MUTATED	69	59	20
DEL PEAK 43(16P13.3) WILD-TYPE	97	151	229

Figure S532. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.018

Table S533. Gene #82: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 43(16P13.3) MUTATED	58	50	31
DEL PEAK 43(16P13.3) WILD-TYPE	190	107	141

Figure S533. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S534. Gene #82: 'del_16p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 43(16P13.3) MUTATED	38	30	9	13	15
DEL PEAK 43(16P13.3) WILD-TYPE	37	120	16	76	101

Figure S534. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00062

Table S535. Gene #82: 'del_16p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 43(16P13.3) MUTATED	56	72	19
DEL PEAK 43(16P13.3) WILD-TYPE	108	256	112

Figure S535. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S536. Gene #82: 'del_16p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 43(16P13.3) MUTATED	60	20	44	15	8
DEL PEAK 43(16P13.3) WILD-TYPE	67	85	185	80	59

Figure S536. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00234 (Fisher's exact test), Q value = 0.0036

Table S537. Gene #82: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 43(16P13.3) MUTATED	49	49	29
DEL PEAK 43(16P13.3) WILD-TYPE	95	160	142

Figure S537. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S538. Gene #82: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 43(16P13.3) MUTATED	30	39	27	16	15
DEL PEAK 43(16P13.3) WILD-TYPE	17	83	135	85	77

Figure S538. Get High-res Image Gene #82: 'del_16p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S539. Gene #83: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 44(16Q23.1) MUTATED	109	91	65
DEL PEAK 44(16Q23.1) WILD-TYPE	57	119	184

Figure S539. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0012

Table S540. Gene #83: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 44(16Q23.1) MUTATED	125	65	55
DEL PEAK 44(16Q23.1) WILD-TYPE	123	92	117

Figure S540. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S541. Gene #83: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 44(16Q23.1) MUTATED	50	63	15	19	41
DEL PEAK 44(16Q23.1) WILD-TYPE	25	87	10	70	75

Figure S541. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.0049

Table S542. Gene #83: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 44(16Q23.1) MUTATED	68	156	40
DEL PEAK 44(16Q23.1) WILD-TYPE	96	172	91

Figure S542. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S543. Gene #83: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 44(16Q23.1) MUTATED	74	51	97	21	21
DEL PEAK 44(16Q23.1) WILD-TYPE	53	54	132	74	46

Figure S543. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.013

Table S544. Gene #83: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 44(16Q23.1) MUTATED	64	100	56
DEL PEAK 44(16Q23.1) WILD-TYPE	80	109	115

Figure S544. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S545. Gene #83: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 44(16Q23.1) MUTATED	32	67	65	35	21
DEL PEAK 44(16Q23.1) WILD-TYPE	15	55	97	66	71

Figure S545. Get High-res Image Gene #83: 'del_16q23.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S546. Gene #84: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 45(17P12) MUTATED	121	103	43
DEL PEAK 45(17P12) WILD-TYPE	45	107	206

Figure S546. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #1: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S547. Gene #84: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 45(17P12) MUTATED	120	80	51
DEL PEAK 45(17P12) WILD-TYPE	128	77	121

Figure S547. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.0032

Table S548. Gene #84: 'del_17p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 45(17P12) MUTATED	110	50	24
DEL PEAK 45(17P12) WILD-TYPE	124	79	68

Figure S548. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S549. Gene #84: 'del_17p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 45(17P12) MUTATED	51	62	15	27	29
DEL PEAK 45(17P12) WILD-TYPE	24	88	10	62	87

Figure S549. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.00096

Table S550. Gene #84: 'del_17p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 45(17P12) MUTATED	74	155	37
DEL PEAK 45(17P12) WILD-TYPE	90	173	94

Figure S550. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S551. Gene #84: 'del_17p12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 45(17P12) MUTATED	87	46	92	27	14
DEL PEAK 45(17P12) WILD-TYPE	40	59	137	68	53

Figure S551. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S552. Gene #84: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 45(17P12) MUTATED	33	70	67	30	28
DEL PEAK 45(17P12) WILD-TYPE	14	52	95	71	64

Figure S552. Get High-res Image Gene #84: 'del_17p12' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S553. Gene #85: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 46(17Q24.3) MUTATED	48	36	19
DEL PEAK 46(17Q24.3) WILD-TYPE	118	174	230

Figure S553. Get High-res Image Gene #85: 'del_17q24.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_17q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.013

Table S554. Gene #85: 'del_17q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 46(17Q24.3) MUTATED	22	21	4	13	11
DEL PEAK 46(17Q24.3) WILD-TYPE	53	129	21	76	105

Figure S554. Get High-res Image Gene #85: 'del_17q24.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_17q24.3' versus 'MIRSEQ_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.047

Table S555. Gene #85: 'del_17q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 46(17Q24.3) MUTATED	23	65	14
DEL PEAK 46(17Q24.3) WILD-TYPE	141	263	117

Figure S555. Get High-res Image Gene #85: 'del_17q24.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S556. Gene #86: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 47(18Q12.2) MUTATED	107	132	53
DEL PEAK 47(18Q12.2) WILD-TYPE	59	78	196

Figure S556. Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q12.2' versus 'METHLYATION_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0027

Table S557. Gene #86: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 47(18Q12.2) MUTATED	119	88	63
DEL PEAK 47(18Q12.2) WILD-TYPE	129	69	109

Figure S557. Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q12.2' versus 'MIRSEQ_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.041

Table S558. Gene #86: 'del_18q12.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 47(18Q12.2) MUTATED	86	157	49
DEL PEAK 47(18Q12.2) WILD-TYPE	78	171	82

Figure S558. Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_18q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0036

Table S559. Gene #86: 'del_18q12.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 47(18Q12.2) MUTATED	75	41	100	52	24
DEL PEAK 47(18Q12.2) WILD-TYPE	52	64	129	43	43

Figure S559. Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_18q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.033

Table S560. Gene #86: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 47(18Q12.2) MUTATED	28	61	72	36	50
DEL PEAK 47(18Q12.2) WILD-TYPE	19	61	90	65	42

Figure S560. Get High-res Image Gene #86: 'del_18q12.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S561. Gene #87: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 48(18Q21.2) MUTATED	116	145	62
DEL PEAK 48(18Q21.2) WILD-TYPE	50	65	187

Figure S561. Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00081

Table S562. Gene #87: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 48(18Q21.2) MUTATED	138	94	69
DEL PEAK 48(18Q21.2) WILD-TYPE	110	63	103

Figure S562. Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0414 (Fisher's exact test), Q value = 0.051

Table S563. Gene #87: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 48(18Q21.2) MUTATED	46	73	18	49	52
DEL PEAK 48(18Q21.2) WILD-TYPE	29	77	7	40	64

Figure S563. Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.018

Table S564. Gene #87: 'del_18q21.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 48(18Q21.2) MUTATED	91	179	53
DEL PEAK 48(18Q21.2) WILD-TYPE	73	149	78

Figure S564. Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00443 (Fisher's exact test), Q value = 0.0065

Table S565. Gene #87: 'del_18q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 48(18Q21.2) MUTATED	81	50	111	55	26
DEL PEAK 48(18Q21.2) WILD-TYPE	46	55	118	40	41

Figure S565. Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.05

Table S566. Gene #87: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 48(18Q21.2) MUTATED	27	72	79	41	53
DEL PEAK 48(18Q21.2) WILD-TYPE	20	50	83	60	39

Figure S566. Get High-res Image Gene #87: 'del_18q21.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S567. Gene #88: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 49(19P13.3) MUTATED	111	113	25
DEL PEAK 49(19P13.3) WILD-TYPE	55	97	224

Figure S567. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S568. Gene #88: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 49(19P13.3) MUTATED	92	96	45
DEL PEAK 49(19P13.3) WILD-TYPE	156	61	127

Figure S568. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S569. Gene #88: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 49(19P13.3) MUTATED	94	64	14
DEL PEAK 49(19P13.3) WILD-TYPE	140	65	78

Figure S569. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S570. Gene #88: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 49(19P13.3) MUTATED	55	50	12	38	17
DEL PEAK 49(19P13.3) WILD-TYPE	20	100	13	51	99

Figure S570. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S571. Gene #88: 'del_19p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 49(19P13.3) MUTATED	96	125	27
DEL PEAK 49(19P13.3) WILD-TYPE	68	203	104

Figure S571. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S572. Gene #88: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 49(19P13.3) MUTATED	100	35	63	43	7
DEL PEAK 49(19P13.3) WILD-TYPE	27	70	166	52	60

Figure S572. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S573. Gene #88: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 49(19P13.3) MUTATED	89	81	44
DEL PEAK 49(19P13.3) WILD-TYPE	55	128	127

Figure S573. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S574. Gene #88: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 49(19P13.3) MUTATED	37	65	46	24	42
DEL PEAK 49(19P13.3) WILD-TYPE	10	57	116	77	50

Figure S574. Get High-res Image Gene #88: 'del_19p13.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S575. Gene #89: 'del_19q13.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 50(19Q13.11) MUTATED	58	51	11
DEL PEAK 50(19Q13.11) WILD-TYPE	108	159	238

Figure S575. Get High-res Image Gene #89: '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 = 2.4e-05

Table S576. Gene #89: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 50(19Q13.11) MUTATED	38	63	12
DEL PEAK 50(19Q13.11) WILD-TYPE	210	94	160

Figure S576. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.11' versus 'MRNASEQ_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0024

Table S577. Gene #89: 'del_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 50(19Q13.11) MUTATED	40	35	8
DEL PEAK 50(19Q13.11) WILD-TYPE	194	94	84

Figure S577. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S578. Gene #89: 'del_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 50(19Q13.11) MUTATED	27	24	1	24	7
DEL PEAK 50(19Q13.11) WILD-TYPE	48	126	24	65	109

Figure S578. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S579. Gene #89: 'del_19q13.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 50(19Q13.11) MUTATED	52	54	13
DEL PEAK 50(19Q13.11) WILD-TYPE	112	274	118

Figure S579. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_19q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S580. Gene #89: 'del_19q13.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 50(19Q13.11) MUTATED	47	19	24	27	2
DEL PEAK 50(19Q13.11) WILD-TYPE	80	86	205	68	65

Figure S580. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S581. Gene #89: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 50(19Q13.11) MUTATED	46	38	20
DEL PEAK 50(19Q13.11) WILD-TYPE	98	171	151

Figure S581. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00058

Table S582. Gene #89: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 50(19Q13.11) MUTATED	16	28	19	14	27
DEL PEAK 50(19Q13.11) WILD-TYPE	31	94	143	87	65

Figure S582. Get High-res Image Gene #89: 'del_19q13.11' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S583. Gene #90: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 51(20P12.1) MUTATED	19	39	14
DEL PEAK 51(20P12.1) WILD-TYPE	147	171	235

Figure S583. Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.035

Table S584. Gene #90: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 51(20P12.1) MUTATED	28	28	14
DEL PEAK 51(20P12.1) WILD-TYPE	220	129	158

Figure S584. Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00317 (Fisher's exact test), Q value = 0.0048

Table S585. Gene #90: 'del_20p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 51(20P12.1) MUTATED	26	9	23	12	2
DEL PEAK 51(20P12.1) WILD-TYPE	101	96	206	83	65

Figure S585. Get High-res Image Gene #90: 'del_20p12.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S586. Gene #91: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 52(21Q11.2) MUTATED	103	125	62
DEL PEAK 52(21Q11.2) WILD-TYPE	63	85	187

Figure S586. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.015

Table S587. Gene #91: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 52(21Q11.2) MUTATED	121	87	67
DEL PEAK 52(21Q11.2) WILD-TYPE	127	70	105

Figure S587. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S588. Gene #91: 'del_21q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 52(21Q11.2) MUTATED	96	75	29
DEL PEAK 52(21Q11.2) WILD-TYPE	138	54	63

Figure S588. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S589. Gene #91: 'del_21q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 52(21Q11.2) MUTATED	48	53	18	48	33
DEL PEAK 52(21Q11.2) WILD-TYPE	27	97	7	41	83

Figure S589. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S590. Gene #91: 'del_21q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 52(21Q11.2) MUTATED	95	150	45
DEL PEAK 52(21Q11.2) WILD-TYPE	69	178	86

Figure S590. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S591. Gene #91: 'del_21q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 52(21Q11.2) MUTATED	77	35	105	52	21
DEL PEAK 52(21Q11.2) WILD-TYPE	50	70	124	43	46

Figure S591. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.006

Table S592. Gene #91: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 52(21Q11.2) MUTATED	85	98	69
DEL PEAK 52(21Q11.2) WILD-TYPE	59	111	102

Figure S592. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00159 (Fisher's exact test), Q value = 0.0026

Table S593. Gene #91: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 52(21Q11.2) MUTATED	31	66	62	42	51
DEL PEAK 52(21Q11.2) WILD-TYPE	16	56	100	59	41

Figure S593. Get High-res Image Gene #91: 'del_21q11.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q22.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S594. Gene #92: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 53(21Q22.13) MUTATED	104	136	65
DEL PEAK 53(21Q22.13) WILD-TYPE	62	74	184

Figure S594. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #1: 'CN_CNMF'

'del_21q22.13' versus 'METHLYATION_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.028

Table S595. Gene #92: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 53(21Q22.13) MUTATED	132	84	70
DEL PEAK 53(21Q22.13) WILD-TYPE	116	73	102

Figure S595. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_21q22.13' versus 'MRNASEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0012

Table S596. Gene #92: 'del_21q22.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 53(21Q22.13) MUTATED	101	76	32
DEL PEAK 53(21Q22.13) WILD-TYPE	133	53	60

Figure S596. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_21q22.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S597. Gene #92: 'del_21q22.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 53(21Q22.13) MUTATED	46	59	18	48	38
DEL PEAK 53(21Q22.13) WILD-TYPE	29	91	7	41	78

Figure S597. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0023

Table S598. Gene #92: 'del_21q22.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 53(21Q22.13) MUTATED	93	165	47
DEL PEAK 53(21Q22.13) WILD-TYPE	71	163	84

Figure S598. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_21q22.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0018

Table S599. Gene #92: 'del_21q22.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 53(21Q22.13) MUTATED	77	42	112	52	22
DEL PEAK 53(21Q22.13) WILD-TYPE	50	63	117	43	45

Figure S599. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0054

Table S600. Gene #92: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 53(21Q22.13) MUTATED	88	103	72
DEL PEAK 53(21Q22.13) WILD-TYPE	56	106	99

Figure S600. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_21q22.13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.017

Table S601. Gene #92: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 53(21Q22.13) MUTATED	29	71	70	42	51
DEL PEAK 53(21Q22.13) WILD-TYPE	18	51	92	59	41

Figure S601. Get High-res Image Gene #92: 'del_21q22.13' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S602. Gene #93: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 54(22Q11.1) MUTATED	101	97	32
DEL PEAK 54(22Q11.1) WILD-TYPE	65	113	217

Figure S602. Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q11.1' versus 'METHLYATION_CNMF'

P value = 0.00596 (Fisher's exact test), Q value = 0.0085

Table S603. Gene #93: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 54(22Q11.1) MUTATED	99	67	47
DEL PEAK 54(22Q11.1) WILD-TYPE	149	90	125

Figure S603. Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q11.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S604. Gene #93: 'del_22q11.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 54(22Q11.1) MUTATED	46	55	12	23	27
DEL PEAK 54(22Q11.1) WILD-TYPE	29	95	13	66	89

Figure S604. Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_CNMF'

P value = 0.00185 (Fisher's exact test), Q value = 0.003

Table S605. Gene #93: 'del_22q11.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 54(22Q11.1) MUTATED	66	132	31
DEL PEAK 54(22Q11.1) WILD-TYPE	98	196	100

Figure S605. Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_22q11.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S606. Gene #93: 'del_22q11.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 54(22Q11.1) MUTATED	77	37	75	25	15
DEL PEAK 54(22Q11.1) WILD-TYPE	50	68	154	70	52

Figure S606. Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_22q11.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S607. Gene #93: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 54(22Q11.1) MUTATED	27	60	50	31	24
DEL PEAK 54(22Q11.1) WILD-TYPE	20	62	112	70	68

Figure S607. Get High-res Image Gene #93: 'del_22q11.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S608. Gene #94: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 55(22Q13.31) MUTATED	96	106	33
DEL PEAK 55(22Q13.31) WILD-TYPE	70	104	216

Figure S608. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_22q13.31' versus 'METHLYATION_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0041

Table S609. Gene #94: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 55(22Q13.31) MUTATED	98	72	48
DEL PEAK 55(22Q13.31) WILD-TYPE	150	85	124

Figure S609. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_22q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S610. Gene #94: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 55(22Q13.31) MUTATED	46	55	11	24	29
DEL PEAK 55(22Q13.31) WILD-TYPE	29	95	14	65	87

Figure S610. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S611. Gene #94: 'del_22q13.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 55(22Q13.31) MUTATED	67	138	29
DEL PEAK 55(22Q13.31) WILD-TYPE	97	190	102

Figure S611. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_22q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S612. Gene #94: 'del_22q13.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 55(22Q13.31) MUTATED	78	38	76	27	15
DEL PEAK 55(22Q13.31) WILD-TYPE	49	67	153	68	52

Figure S612. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.037

Table S613. Gene #94: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 55(22Q13.31) MUTATED	61	89	52
DEL PEAK 55(22Q13.31) WILD-TYPE	83	120	119

Figure S613. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_22q13.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S614. Gene #94: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 55(22Q13.31) MUTATED	29	62	54	31	26
DEL PEAK 55(22Q13.31) WILD-TYPE	18	60	108	70	66

Figure S614. Get High-res Image Gene #94: 'del_22q13.31' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S615. Gene #95: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 56(XP22.2) MUTATED	51	81	18
DEL PEAK 56(XP22.2) WILD-TYPE	115	129	231

Figure S615. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S616. Gene #95: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 56(XP22.2) MUTATED	57	60	27
DEL PEAK 56(XP22.2) WILD-TYPE	191	97	145

Figure S616. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00071

Table S617. Gene #95: 'del_xp22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 56(XP22.2) MUTATED	55	48	13
DEL PEAK 56(XP22.2) WILD-TYPE	179	81	79

Figure S617. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.6e-05

Table S618. Gene #95: 'del_xp22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 56(XP22.2) MUTATED	25	32	8	36	15
DEL PEAK 56(XP22.2) WILD-TYPE	50	118	17	53	101

Figure S618. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S619. Gene #95: 'del_xp22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 56(XP22.2) MUTATED	60	73	17
DEL PEAK 56(XP22.2) WILD-TYPE	104	255	114

Figure S619. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S620. Gene #95: 'del_xp22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 56(XP22.2) MUTATED	43	18	43	39	7
DEL PEAK 56(XP22.2) WILD-TYPE	84	87	186	56	60

Figure S620. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0023

Table S621. Gene #95: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 56(XP22.2) MUTATED	14	33	33	19	39
DEL PEAK 56(XP22.2) WILD-TYPE	33	89	129	82	53

Figure S621. Get High-res Image Gene #95: 'del_xp22.2' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S622. Gene #96: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 57(XP21.1) MUTATED	47	83	13
DEL PEAK 57(XP21.1) WILD-TYPE	119	127	236

Figure S622. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.6e-05

Table S623. Gene #96: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 57(XP21.1) MUTATED	54	57	24
DEL PEAK 57(XP21.1) WILD-TYPE	194	100	148

Figure S623. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S624. Gene #96: 'del_xp21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 57(XP21.1) MUTATED	45	53	11
DEL PEAK 57(XP21.1) WILD-TYPE	189	76	81

Figure S624. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S625. Gene #96: 'del_xp21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 57(XP21.1) MUTATED	24	24	8	39	14
DEL PEAK 57(XP21.1) WILD-TYPE	51	126	17	50	102

Figure S625. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S626. Gene #96: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 57(XP21.1) MUTATED	60	69	14
DEL PEAK 57(XP21.1) WILD-TYPE	104	259	117

Figure S626. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.7e-05

Table S627. Gene #96: 'del_xp21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 57(XP21.1) MUTATED	34	17	43	41	8
DEL PEAK 57(XP21.1) WILD-TYPE	93	88	186	54	59

Figure S627. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00694 (Fisher's exact test), Q value = 0.0098

Table S628. Gene #96: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 57(XP21.1) MUTATED	50	45	35
DEL PEAK 57(XP21.1) WILD-TYPE	94	164	136

Figure S628. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00011

Table S629. Gene #96: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 57(XP21.1) MUTATED	14	30	27	18	41
DEL PEAK 57(XP21.1) WILD-TYPE	33	92	135	83	51

Figure S629. Get High-res Image Gene #96: 'del_xp21.1' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S630. Gene #97: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 58(XP11.3) MUTATED	44	90	12
DEL PEAK 58(XP11.3) WILD-TYPE	122	120	237

Figure S630. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S631. Gene #97: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 58(XP11.3) MUTATED	55	61	22
DEL PEAK 58(XP11.3) WILD-TYPE	193	96	150

Figure S631. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S632. Gene #97: 'del_xp11.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 58(XP11.3) MUTATED	48	57	8
DEL PEAK 58(XP11.3) WILD-TYPE	186	72	84

Figure S632. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S633. Gene #97: 'del_xp11.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 58(XP11.3) MUTATED	23	25	8	45	12
DEL PEAK 58(XP11.3) WILD-TYPE	52	125	17	44	104

Figure S633. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S634. Gene #97: 'del_xp11.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 58(XP11.3) MUTATED	61	72	13
DEL PEAK 58(XP11.3) WILD-TYPE	103	256	118

Figure S634. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S635. Gene #97: 'del_xp11.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 58(XP11.3) MUTATED	34	18	41	47	6
DEL PEAK 58(XP11.3) WILD-TYPE	93	87	188	48	61

Figure S635. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00469 (Fisher's exact test), Q value = 0.0068

Table S636. Gene #97: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 58(XP11.3) MUTATED	51	47	34
DEL PEAK 58(XP11.3) WILD-TYPE	93	162	137

Figure S636. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S637. Gene #97: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	47	122	162	101	92
DEL PEAK 58(XP11.3) MUTATED	11	32	27	15	47
DEL PEAK 58(XP11.3) WILD-TYPE	36	90	135	86	45

Figure S637. Get High-res Image Gene #97: 'del_xp11.3' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S638. Gene #98: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 59(XQ11.2) MUTATED	37	54	12
DEL PEAK 59(XQ11.2) WILD-TYPE	129	156	237

Figure S638. Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq11.2' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.024

Table S639. Gene #98: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 59(XQ11.2) MUTATED	43	34	18
DEL PEAK 59(XQ11.2) WILD-TYPE	205	123	154

Figure S639. Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq11.2' versus 'MRNASEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.00094

Table S640. Gene #98: 'del_xq11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 59(XQ11.2) MUTATED	40	31	5
DEL PEAK 59(XQ11.2) WILD-TYPE	194	98	87

Figure S640. Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00453 (Fisher's exact test), Q value = 0.0066

Table S641. Gene #98: 'del_xq11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 59(XQ11.2) MUTATED	19	23	7	18	9
DEL PEAK 59(XQ11.2) WILD-TYPE	56	127	18	71	107

Figure S641. Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq11.2' versus 'MIRSEQ_CNMF'

P value = 0.00447 (Fisher's exact test), Q value = 0.0065

Table S642. Gene #98: 'del_xq11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 59(XQ11.2) MUTATED	33	60	10
DEL PEAK 59(XQ11.2) WILD-TYPE	131	268	121

Figure S642. Get High-res Image Gene #98: 'del_xq11.2' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.4e-05

Table S643. Gene #99: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	166	210	249
DEL PEAK 60(XQ21.33) MUTATED	37	47	12
DEL PEAK 60(XQ21.33) WILD-TYPE	129	163	237

Figure S643. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #1: 'CN_CNMF'

'del_xq21.33' versus 'METHLYATION_CNMF'

P value = 0.00756 (Fisher's exact test), Q value = 0.011

Table S644. Gene #99: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	248	157	172
DEL PEAK 60(XQ21.33) MUTATED	38	34	16
DEL PEAK 60(XQ21.33) WILD-TYPE	210	123	156

Figure S644. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_xq21.33' versus 'MRNASEQ_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.011

Table S645. Gene #99: 'del_xq21.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	129	92
DEL PEAK 60(XQ21.33) MUTATED	41	27	6
DEL PEAK 60(XQ21.33) WILD-TYPE	193	102	86

Figure S645. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_xq21.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00998 (Fisher's exact test), Q value = 0.014

Table S646. Gene #99: 'del_xq21.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	75	150	25	89	116
DEL PEAK 60(XQ21.33) MUTATED	20	24	5	16	9
DEL PEAK 60(XQ21.33) WILD-TYPE	55	126	20	73	107

Figure S646. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.014

Table S647. Gene #99: 'del_xq21.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	164	328	131
DEL PEAK 60(XQ21.33) MUTATED	32	54	10
DEL PEAK 60(XQ21.33) WILD-TYPE	132	274	121

Figure S647. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_xq21.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.048

Table S648. Gene #99: 'del_xq21.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	127	105	229	95	67
DEL PEAK 60(XQ21.33) MUTATED	27	18	30	17	4
DEL PEAK 60(XQ21.33) WILD-TYPE	100	87	199	78	63

Figure S648. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_xq21.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.051

Table S649. Gene #99: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	209	171
DEL PEAK 60(XQ21.33) MUTATED	31	31	19
DEL PEAK 60(XQ21.33) WILD-TYPE	113	178	152

Figure S649. Get High-res Image Gene #99: 'del_xq21.33' versus Molecular Subtype #7: 'MIRSEQ_MATURE_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/STES-TP/15101925/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STES-TP/15125163/STES-TP.transferedmergedcluster.txt
Number of patients = 625
Number of significantly focal cnvs = 99
Number of molecular subtypes = 8
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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