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

Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

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/C1KS6QVF

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 100 focal events and 12 molecular subtypes across 539 patients, 1073 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p35.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q22 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q44 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_2p24.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q13 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3p14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_3q26.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4p16.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5q35.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p24.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6p22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q25.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7q31.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.22 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9p24.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_9q34.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_11p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q13.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q13.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q24.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q32.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_16p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p13 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20q13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_22q12.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xp11.23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_1p36.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.11 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_3p14.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3q13.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4p16.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p15.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q34.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q11.22 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q14.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q11 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q15.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q23.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q21.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19p12 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.43 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 100 focal events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 1073 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1p34 2	73 (14%)	466	0.0129 (0.0151)	0.00097 (0.00128)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00186 (0.00238)	1e-05 (1.62e-05)
amp 1p22 3	96 (18%)	443	0.0194 (0.0224)	0.0148 (0.0172)	1e-05 (1.62e-05)	0.00066 (0.000885)	0.00211 (0.00269)	0.0326 (0.0369)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	3e-05 (4.6e-05)	0.00029 (0.000401)	1e-05 (1.62e-05)
amp 1q21 3	242 (45%)	297	0.0146 (0.017)	0.00585 (0.00715)	1e-05 (1.62e-05)	0.00026 (0.000363)	0.0185 (0.0215)	0.0246 (0.0282)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00448 (0.00551)	3e-05 (4.6e-05)
amp 3q26 2	175 (32%)	364	0.00011 (0.000159)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 3q26 2	164 (30%)	375	0.00029 (0.000401)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 6p24 2	117 (22%)	422	0.00316 (0.00393)	0.00051 (0.000694)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	4e-05 (6.04e-05)
amp 8p11 21	162 (30%)	377	0.0101 (0.0121)	0.0307 (0.0349)	1e-05 (1.62e-05)	0.00311 (0.00388)	0.0003 (0.000414)	0.0001 (0.000145)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	8e-05 (0.000117)	0.00177 (0.00227)
amp 8q24 21	215 (40%)	324	0.00277 (0.00347)	0.00605 (0.00737)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)
amp 11p11 2	51 (9%)	488	0.00212 (0.0027)	0.00814 (0.00981)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00867 (0.0104)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0237 (0.0272)	0.0407 (0.0457)
amp 16p11 2	66 (12%)	473	0.00791 (0.00956)	0.00502 (0.00615)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00022 (0.000309)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00307 (0.00383)	0.00058 (0.000785)
amp 17q25 1	105 (19%)	434	5e-05 (7.44e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	5e-05 (7.44e-05)
amp 19p13 2	99 (18%)	440	0.00405 (0.00499)	0.00016 (0.000228)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 19q12	121 (22%)	418	0.00511 (0.00626)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 20q11 21	152 (28%)	387	0.00058 (0.000785)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 20q13 12	152 (28%)	387	0.0132 (0.0154)	0.00954 (0.0114)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 20q13 33	153 (28%)	386	0.00864 (0.0104)	0.00135 (0.00175)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 1p36 21	71 (13%)	468	0.0246 (0.0282)	0.00176 (0.00226)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00025 (0.000349)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00147 (0.00189)	0.00025 (0.000349)
del 2q22 1	48 (9%)	491	0.039 (0.0439)	0.00067 (0.000896)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00103 (0.00135)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00091 (0.0012)	0.00104 (0.00137)
del 4p16 3	94 (17%)	445	0.0129 (0.0152)	0.00136 (0.00176)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	6e-05 (8.82e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)
del 4p15 2	98 (18%)	441	0.013 (0.0152)	0.0097 (0.0116)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 4q22 1	106 (20%)	433	0.00398 (0.00491)	0.00014 (0.000201)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 4q34 3	130 (24%)	409	0.00398 (0.00491)	0.00015 (0.000215)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 5q12 1	111 (21%)	428	0.0129 (0.0152)	0.00925 (0.0111)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 7p22 3	72 (13%)	467	9e-05 (0.000131)	0.00174 (0.00223)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00019 (0.00027)	2e-05 (3.12e-05)
del 8p23 2	119 (22%)	420	0.00219 (0.00278)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 8p21 2	117 (22%)	422	0.00197 (0.00251)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 9q21 2	129 (24%)	410	5e-05 (7.44e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00029 (0.000401)	1e-05 (1.62e-05)
del 9q34 2	132 (24%)	407	3e-05 (4.6e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00022 (0.000309)	1e-05 (1.62e-05)
del 14q13 1	73 (14%)	466	0.00797 (0.00962)	0.00546 (0.00668)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00112 (0.00147)	1e-05 (1.62e-05)
del 15q23	115 (21%)	424	0.00214 (0.00272)	0.00049 (0.000669)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 16p13 3	92 (17%)	447	0.0133 (0.0156)	0.0096 (0.0115)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 16q21	154 (29%)	385	0.00089 (0.00118)	5e-05 (7.44e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 16q22 3	158 (29%)	381	0.0337 (0.0381)	0.0105 (0.0124)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	5e-05 (7.44e-05)	1e-05 (1.62e-05)
del 16q23 1	166 (31%)	373	0.00314 (0.00391)	0.00023 (0.000323)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 17p13 3	122 (23%)	417	0.00081 (0.00107)	3e-05 (4.6e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	6e-05 (8.82e-05)
del 17p11 2	128 (24%)	411	0.00072 (0.000961)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 17q11 2	105 (19%)	434	0.00064 (0.00086)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00386 (0.00478)	0.00304 (0.0038)
del 17q21 31	114 (21%)	425	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00013 (0.000187)	0.00119 (0.00155)
del 19p13 3	154 (29%)	385	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 19q13 43	67 (12%)	472	0.00067 (0.000896)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00018 (0.000257)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00995 (0.0119)	2e-05 (3.12e-05)
del 22q13 32	141 (26%)	398	3e-05 (4.6e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	6e-05 (8.82e-05)	1e-05 (1.62e-05)
del xp21 1	88 (16%)	451	0.00065 (0.000872)	0.00118 (0.00154)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	7e-05 (0.000103)	1e-05 (1.62e-05)
amp 1p35 2	56 (10%)	483	0.0516 (0.0574)	0.00046 (0.000629)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0008 (0.00106)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.037 (0.0418)	0.00014 (0.000201)
amp 1q22	256 (47%)	283	0.0217 (0.0251)	0.0108 (0.0127)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	0.0188 (0.0218)	0.0197 (0.0228)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.053 (0.0588)	0.00013 (0.000187)
amp 2q13	119 (22%)	420	0.161 (0.173)	0.029 (0.0332)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 4p16 3	53 (10%)	486	0.0507 (0.0565)	0.00745 (0.00905)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	3e-05 (4.6e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00133 (0.00173)	0.00041 (0.000563)
amp 5p15 33	89 (17%)	450	0.23 (0.242)	0.0434 (0.0486)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 8q24 21	209 (39%)	330	0.0117 (0.0138)	0.0727 (0.08)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 9q34 3	39 (7%)	500	0.243 (0.255)	0.0143 (0.0168)	1e-05 (1.62e-05)	6e-05 (8.82e-05)	0.0012 (0.00156)	0.00207 (0.00264)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	0.0437 (0.0489)	0.00294 (0.00367)
amp 11q13 2	74 (14%)	465	0.00191 (0.00244)	0.00783 (0.00948)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00045 (0.000616)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	5e-05 (7.44e-05)	2e-05 (3.12e-05)	0.0571 (0.0632)	0.0089 (0.0107)
amp 17q12	75 (14%)	464	0.108 (0.118)	0.00231 (0.00292)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	6e-05 (8.82e-05)	1e-05 (1.62e-05)
del 1p36 11	83 (15%)	456	0.0506 (0.0565)	0.0077 (0.00934)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00102 (0.00134)	1e-05 (1.62e-05)
del 3p14 2	79 (15%)	460	0.0517 (0.0574)	0.00791 (0.00956)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00038 (0.000522)	1e-05 (1.62e-05)
del 9p23	79 (15%)	460	0.38 (0.395)	0.0291 (0.0332)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00255 (0.0032)	0.00081 (0.00107)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0224 (0.0258)	0.00683 (0.00831)
del 13q11	98 (18%)	441	0.334 (0.349)	0.0397 (0.0446)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00081 (0.00107)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0246 (0.0282)	0.00728 (0.00885)
del 15q15 1	140 (26%)	399	0.0509 (0.0567)	0.0104 (0.0124)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 2p24 3	121 (22%)	418	0.68 (0.697)	0.131 (0.142)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	6e-05 (8.82e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00019 (0.00027)	0.00059 (0.000796)
amp 3p25 1	82 (15%)	457	0.19 (0.201)	0.0522 (0.0579)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	5e-05 (7.44e-05)	0.00146 (0.00188)
amp 5q35 3	57 (11%)	482	0.137 (0.148)	0.167 (0.179)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00024 (0.000336)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0006 (0.000808)	0.00119 (0.00155)
amp 6p22 3	107 (20%)	432	0.186 (0.198)	0.115 (0.125)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	2e-05 (3.12e-05)
amp 6q25 1	88 (16%)	451	0.284 (0.298)	1 (1.00)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	9e-05 (0.000131)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	6e-05 (8.82e-05)	0.0307 (0.0349)
amp 7q31 2	93 (17%)	446	0.532 (0.549)	0.435 (0.451)	1e-05 (1.62e-05)	0.00021 (0.000296)	0.0027 (0.00339)	0.00109 (0.00143)	0.0003 (0.000414)	5e-05 (7.44e-05)	0.00119 (0.00155)	0.011 (0.013)	0.0205 (0.0237)	0.0145 (0.017)
amp 9p24 2	65 (12%)	474	0.127 (0.138)	0.0854 (0.0938)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0002 (0.000283)	0.00021 (0.000296)
amp 11q14 1	59 (11%)	480	0.378 (0.393)	0.192 (0.204)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0001 (0.000145)	0.00219 (0.00278)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00012 (0.000174)	2e-05 (3.12e-05)	0.0168 (0.0196)	0.0256 (0.0293)
amp 12p12 1	93 (17%)	446	0.327 (0.341)	0.539 (0.555)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00171 (0.0022)	0.00157 (0.00202)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0005 (0.000682)	1e-05 (1.62e-05)
amp 12q13 11	87 (16%)	452	0.377 (0.393)	0.205 (0.216)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00059 (0.000796)	0.0006 (0.000808)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00124 (0.00161)	0.00036 (0.000495)
amp 12q13 2	100 (19%)	439	0.182 (0.194)	0.0885 (0.0968)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	0.00056 (0.000759)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	0.00016 (0.000228)
amp 13q34	58 (11%)	481	0.689 (0.706)	0.166 (0.178)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	3e-05 (4.6e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00061 (0.000821)	2e-05 (3.12e-05)
amp 14q24 3	64 (12%)	475	0.0608 (0.0672)	0.0107 (0.0126)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0127 (0.015)	0.0118 (0.014)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0642 (0.0709)	0.0455 (0.0508)
amp 14q32 33	79 (15%)	460	0.432 (0.447)	0.315 (0.329)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	9e-05 (0.000131)	0.00032 (0.000441)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00282 (0.00353)	0.0258 (0.0295)
amp 17q11 2	71 (13%)	468	0.151 (0.162)	0.0505 (0.0564)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	3e-05 (4.6e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 18p11 31	96 (18%)	443	0.155 (0.167)	0.0561 (0.0621)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 18q11 2	69 (13%)	470	0.108 (0.118)	0.183 (0.195)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp 20p13	117 (22%)	422	0.15 (0.162)	0.051 (0.0568)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00036 (0.000495)	1e-05 (1.62e-05)
amp 22q12 2	62 (12%)	477	0.381 (0.395)	0.196 (0.207)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
amp xq28	93 (17%)	446	0.0857 (0.094)	0.0268 (0.0306)	1e-05 (1.62e-05)	0.0307 (0.0349)	0.00013 (0.000187)	0.0376 (0.0424)	0.00094 (0.00124)	0.00238 (0.00301)	0.0025 (0.00315)	0.0123 (0.0145)	0.0174 (0.0202)	0.163 (0.175)
del 6q26	46 (9%)	493	0.379 (0.394)	0.0294 (0.0335)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0533 (0.059)	0.00121 (0.00157)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00076 (0.00101)	0.00015 (0.000215)
del 7q11 22	41 (8%)	498			1e-05 (1.62e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	0.00234 (0.00296)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00771 (0.00935)	0.00135 (0.00175)
del 7q31 1	55 (10%)	484	0.138 (0.15)	0.168 (0.179)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	6e-05 (8.82e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00027 (0.000375)	0.00043 (0.00059)
del 7q36 1	63 (12%)	476	0.33 (0.345)	0.0783 (0.0862)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0001 (0.000145)	3e-05 (4.6e-05)
del 10q23 31	77 (14%)	462	0.138 (0.149)	0.166 (0.178)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	5e-05 (7.44e-05)	3e-05 (4.6e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00055 (0.000747)	2e-05 (3.12e-05)
del 11p15 5	106 (20%)	433	0.38 (0.395)	0.195 (0.207)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 11q14 1	70 (13%)	469			1e-05 (1.62e-05)	1e-05 (1.62e-05)	9e-05 (0.000131)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)
del 11q25	93 (17%)	446			1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	3e-05 (4.6e-05)	1e-05 (1.62e-05)
del 12q23 1	56 (10%)	483			1e-05 (1.62e-05)	1e-05 (1.62e-05)	5e-05 (7.44e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	8e-05 (0.000117)	1e-05 (1.62e-05)
del 12q24 33	66 (12%)	473			1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	1e-05 (1.62e-05)
del 13q14 2	107 (20%)	432	0.618 (0.634)	0.0653 (0.0719)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00029 (0.000401)	2e-05 (3.12e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.022 (0.0254)	0.00293 (0.00367)
del 18q21 2	91 (17%)	448	0.619 (0.636)	0.253 (0.266)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00214 (0.00272)	6e-05 (8.82e-05)
del 18q23	98 (18%)	441	0.616 (0.633)	0.252 (0.265)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00024 (0.000336)	0.00014 (0.000201)
del 19p12	58 (11%)	481			1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00603 (0.00735)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.0329 (0.0372)	2e-05 (3.12e-05)
amp 1q44	218 (40%)	321	0.032 (0.0364)	0.0385 (0.0433)	1e-05 (1.62e-05)	0.0373 (0.042)	0.457 (0.472)	0.0232 (0.0267)	0.00154 (0.00198)	0.00072 (0.000961)	1e-05 (1.62e-05)	0.00603 (0.00735)	0.867 (0.883)	0.0649 (0.0716)
amp 3p14 1	65 (12%)	474	0.535 (0.551)	0.511 (0.528)	1e-05 (1.62e-05)	0.00027 (0.000375)	0.00977 (0.0117)	0.0186 (0.0216)	1e-05 (1.62e-05)	2e-05 (3.12e-05)	3e-05 (4.6e-05)	1e-05 (1.62e-05)	0.00321 (0.00399)	0.17 (0.181)
amp xp11 23	90 (17%)	449	0.358 (0.374)	0.814 (0.831)	1e-05 (1.62e-05)	0.0002 (0.000283)	0.00326 (0.00405)	0.0912 (0.0997)	0.00019 (0.00027)	0.00044 (0.000603)	0.00022 (0.000309)	0.00243 (0.00307)	0.00915 (0.011)	0.00998 (0.0119)
del 3q13 31	43 (8%)	496	0.62 (0.636)	0.184 (0.196)	1e-05 (1.62e-05)	0.00051 (0.000694)	0.00455 (0.00559)	0.00407 (0.00501)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	3e-05 (4.6e-05)	5e-05 (7.44e-05)	0.0154 (0.0179)	0.31 (0.324)
del 2q37 3	53 (10%)	486			1e-05 (1.62e-05)	1e-05 (1.62e-05)	4e-05 (6.04e-05)	0.00479 (0.00588)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	1e-05 (1.62e-05)	0.00077 (0.00102)	0.198 (0.209)	0.128 (0.139)
amp 15q26 3	38 (7%)	501			1e-05 (1.62e-05)	0.00858 (0.0103)	0.00386 (0.00478)	0.082 (0.0901)	1e-05 (1.62e-05)	3e-05 (4.6e-05)	0.00011 (0.000159)	0.00015 (0.000215)	0.12 (0.131)	0.166 (0.178)
del 2p25 3	26 (5%)	513			1e-05 (1.62e-05)	0.00015 (0.000215)	0.00395 (0.00488)	0.11 (0.12)	6e-05 (8.82e-05)	0.00023 (0.000323)	0.00125 (0.00162)	0.00074 (0.000987)	0.174 (0.185)	0.141 (0.152)
del 20p12 1	36 (7%)	503	1 (1.00)	0.514 (0.53)	1e-05 (1.62e-05)	0.0424 (0.0476)	0.497 (0.514)	0.00252 (0.00317)	0.00027 (0.000375)	0.00137 (0.00177)	0.00053 (0.00072)	0.00079 (0.00105)	0.0872 (0.0955)	0.189 (0.201)
amp 10q22 2	143 (27%)	396	0.0322 (0.0365)	0.115 (0.125)	1e-05 (1.62e-05)	0.185 (0.196)	0.00367 (0.00455)	0.288 (0.302)	0.0137 (0.016)	0.00248 (0.00313)	0.859 (0.876)	0.0128 (0.0151)	0.977 (0.994)	0.189 (0.201)
amp 8p11 22	126 (23%)	413	0.0869 (0.0953)	0.223 (0.235)	1e-05 (1.62e-05)	1 (1.00)	0.283 (0.297)	0.00021 (0.000296)	0.12 (0.131)	0.00806 (0.00972)	0.701 (0.718)	0.0364 (0.0411)	0.725 (0.741)	0.749 (0.765)

'amp_1p35.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.00063

Table S1. Gene #1: 'amp_1p35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 1(1P35.2) MUTATED	1	5	0	0	0
AMP PEAK 1(1P35.2) WILD-TYPE	13	4	7	7	16

Figure S1. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S2. Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 1(1P35.2) MUTATED	54	0	1	0	1
AMP PEAK 1(1P35.2) WILD-TYPE	115	305	18	9	36

Figure S2. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S3. Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 1(1P35.2) MUTATED	35	4	6
AMP PEAK 1(1P35.2) WILD-TYPE	130	85	165

Figure S3. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p35.2' versus 'RPPA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0011

Table S4. Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 1(1P35.2) MUTATED	5	12	27
AMP PEAK 1(1P35.2) WILD-TYPE	120	139	130

Figure S4. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p35.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S5. Gene #1: 'amp_1p35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 1(1P35.2) MUTATED	0	34	6	4
AMP PEAK 1(1P35.2) WILD-TYPE	108	148	87	46

Figure S5. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S6. Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 1(1P35.2) MUTATED	49	0	6
AMP PEAK 1(1P35.2) WILD-TYPE	185	153	144

Figure S6. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S7. Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 1(1P35.2) MUTATED	36	0	7	0	7	5	0
AMP PEAK 1(1P35.2) WILD-TYPE	87	53	40	65	101	61	75

Figure S7. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S8. Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 1(1P35.2) MUTATED	42	6	5
AMP PEAK 1(1P35.2) WILD-TYPE	181	144	152

Figure S8. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S9. Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 1(1P35.2) MUTATED	18	0	5	30
AMP PEAK 1(1P35.2) WILD-TYPE	201	58	132	86

Figure S9. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.042

Table S10. Gene #1: 'amp_1p35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 1(1P35.2) MUTATED	26	6	10
AMP PEAK 1(1P35.2) WILD-TYPE	146	90	120

Figure S10. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 2e-04

Table S11. Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 1(1P35.2) MUTATED	28	6	8
AMP PEAK 1(1P35.2) WILD-TYPE	116	109	131

Figure S11. Get High-res Image Gene #1: 'amp_1p35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p34.2' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.015

Table S12. Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 2(1P34.2) MUTATED	1	6	0	0
AMP PEAK 2(1P34.2) WILD-TYPE	13	11	12	10

Figure S12. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p34.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00097 (Fisher's exact test), Q value = 0.0013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 2(1P34.2) MUTATED	2	5	0	0	0
AMP PEAK 2(1P34.2) WILD-TYPE	12	4	7	7	16

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

'amp_1p34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S14. Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 2(1P34.2) MUTATED	71	0	1	0	1
AMP PEAK 2(1P34.2) WILD-TYPE	98	305	18	9	36

Figure S14. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S15. Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 2(1P34.2) MUTATED	48	10	5
AMP PEAK 2(1P34.2) WILD-TYPE	117	79	166

Figure S15. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S16. Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 2(1P34.2) MUTATED	7	13	36
AMP PEAK 2(1P34.2) WILD-TYPE	118	138	121

Figure S16. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S17. Gene #2: 'amp_1p34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 2(1P34.2) MUTATED	0	36	16	4
AMP PEAK 2(1P34.2) WILD-TYPE	108	146	77	46

Figure S17. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S18. Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 2(1P34.2) MUTATED	65	1	6
AMP PEAK 2(1P34.2) WILD-TYPE	169	152	144

Figure S18. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S19. Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 2(1P34.2) MUTATED	49	0	10	0	8	5	0
AMP PEAK 2(1P34.2) WILD-TYPE	74	53	37	65	100	61	75

Figure S19. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S20. Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 2(1P34.2) MUTATED	61	6	4
AMP PEAK 2(1P34.2) WILD-TYPE	162	144	153

Figure S20. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S21. Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 2(1P34.2) MUTATED	23	0	4	44
AMP PEAK 2(1P34.2) WILD-TYPE	196	58	133	72

Figure S21. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00186 (Fisher's exact test), Q value = 0.0024

Table S22. Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 2(1P34.2) MUTATED	38	10	11
AMP PEAK 2(1P34.2) WILD-TYPE	134	86	119

Figure S22. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S23. Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 2(1P34.2) MUTATED	39	5	15
AMP PEAK 2(1P34.2) WILD-TYPE	105	110	124

Figure S23. Get High-res Image Gene #2: 'amp_1p34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1p22.3' versus 'MRNA_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.022

Table S24. Gene #3: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 3(1P22.3) MUTATED	5	5	0	0
AMP PEAK 3(1P22.3) WILD-TYPE	9	12	12	10

Figure S24. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.017

Table S25. Gene #3: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 3(1P22.3) MUTATED	2	4	1	3	0
AMP PEAK 3(1P22.3) WILD-TYPE	12	5	6	4	16

Figure S25. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S26. Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 3(1P22.3) MUTATED	53	30	2	7	4
AMP PEAK 3(1P22.3) WILD-TYPE	116	275	17	2	33

Figure S26. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1p22.3' versus 'METHLYATION_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.00088

Table S27. Gene #3: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 3(1P22.3) MUTATED	44	8	24
AMP PEAK 3(1P22.3) WILD-TYPE	121	81	147

Figure S27. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0027

Table S28. Gene #3: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 3(1P22.3) MUTATED	16	21	43
AMP PEAK 3(1P22.3) WILD-TYPE	109	130	114

Figure S28. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.037

Table S29. Gene #3: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 3(1P22.3) MUTATED	18	45	11	6
AMP PEAK 3(1P22.3) WILD-TYPE	90	137	82	44

Figure S29. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S30. Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 3(1P22.3) MUTATED	60	27	8
AMP PEAK 3(1P22.3) WILD-TYPE	174	126	142

Figure S30. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S31. Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 3(1P22.3) MUTATED	42	7	8	18	13	4	3
AMP PEAK 3(1P22.3) WILD-TYPE	81	46	39	47	95	62	72

Figure S31. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S32. Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 3(1P22.3) MUTATED	52	36	7
AMP PEAK 3(1P22.3) WILD-TYPE	171	114	150

Figure S32. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S33. Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 3(1P22.3) MUTATED	42	8	10	35
AMP PEAK 3(1P22.3) WILD-TYPE	177	50	127	81

Figure S33. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 4e-04

Table S34. Gene #3: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 3(1P22.3) MUTATED	48	13	14
AMP PEAK 3(1P22.3) WILD-TYPE	124	83	116

Figure S34. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S35. Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 3(1P22.3) MUTATED	46	8	21
AMP PEAK 3(1P22.3) WILD-TYPE	98	107	118

Figure S35. Get High-res Image Gene #3: 'amp_1p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNA_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.017

Table S36. Gene #4: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 4(1Q21.3) MUTATED	11	12	5	2
AMP PEAK 4(1Q21.3) WILD-TYPE	3	5	7	8

Figure S36. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00585 (Fisher's exact test), Q value = 0.0071

Table S37. Gene #4: 'amp_1q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 4(1Q21.3) MUTATED	9	7	6	5	3
AMP PEAK 4(1Q21.3) WILD-TYPE	5	2	1	2	13

Figure S37. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S38. Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 4(1Q21.3) MUTATED	105	90	13	9	25
AMP PEAK 4(1Q21.3) WILD-TYPE	64	215	6	0	12

Figure S38. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00036

Table S39. Gene #4: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 4(1Q21.3) MUTATED	92	31	62
AMP PEAK 4(1Q21.3) WILD-TYPE	73	58	109

Figure S39. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.3' versus 'RPPA_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.021

Table S40. Gene #4: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 4(1Q21.3) MUTATED	55	59	86
AMP PEAK 4(1Q21.3) WILD-TYPE	70	92	71

Figure S40. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.028

Table S41. Gene #4: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 4(1Q21.3) MUTATED	58	90	36	16
AMP PEAK 4(1Q21.3) WILD-TYPE	50	92	57	34

Figure S41. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S42. Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 4(1Q21.3) MUTATED	128	72	42
AMP PEAK 4(1Q21.3) WILD-TYPE	106	81	108

Figure S42. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S43. Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 4(1Q21.3) MUTATED	81	28	22	32	40	18	21
AMP PEAK 4(1Q21.3) WILD-TYPE	42	25	25	33	68	48	54

Figure S43. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S44. Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 4(1Q21.3) MUTATED	113	83	43
AMP PEAK 4(1Q21.3) WILD-TYPE	110	67	114

Figure S44. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S45. Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 4(1Q21.3) MUTATED	94	28	43	74
AMP PEAK 4(1Q21.3) WILD-TYPE	125	30	94	42

Figure S45. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00448 (Fisher's exact test), Q value = 0.0055

Table S46. Gene #4: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 4(1Q21.3) MUTATED	94	40	47
AMP PEAK 4(1Q21.3) WILD-TYPE	78	56	83

Figure S46. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S47. Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 4(1Q21.3) MUTATED	88	37	56
AMP PEAK 4(1Q21.3) WILD-TYPE	56	78	83

Figure S47. Get High-res Image Gene #4: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q22' versus 'MRNA_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.025

Table S48. Gene #5: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 5(1Q22) MUTATED	11	11	5	2
AMP PEAK 5(1Q22) WILD-TYPE	3	6	7	8

Figure S48. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q22' versus 'MRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.013

Table S49. Gene #5: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 5(1Q22) MUTATED	9	6	6	5	3
AMP PEAK 5(1Q22) WILD-TYPE	5	3	1	2	13

Figure S49. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S50. Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 5(1Q22) MUTATED	116	93	13	9	25
AMP PEAK 5(1Q22) WILD-TYPE	53	212	6	0	12

Figure S50. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S51. Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 5(1Q22) MUTATED	100	34	63
AMP PEAK 5(1Q22) WILD-TYPE	65	55	108

Figure S51. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q22' versus 'RPPA_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.022

Table S52. Gene #5: 'amp_1q22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 5(1Q22) MUTATED	57	62	89
AMP PEAK 5(1Q22) WILD-TYPE	68	89	68

Figure S52. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q22' versus 'RPPA_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.023

Table S53. Gene #5: 'amp_1q22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 5(1Q22) MUTATED	60	94	37	17
AMP PEAK 5(1Q22) WILD-TYPE	48	88	56	33

Figure S53. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S54. Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 5(1Q22) MUTATED	137	73	46
AMP PEAK 5(1Q22) WILD-TYPE	97	80	104

Figure S54. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S55. Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 5(1Q22) MUTATED	88	28	23	33	41	20	23
AMP PEAK 5(1Q22) WILD-TYPE	35	25	24	32	67	46	52

Figure S55. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S56. Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 5(1Q22) MUTATED	121	84	48
AMP PEAK 5(1Q22) WILD-TYPE	102	66	109

Figure S56. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S57. Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 5(1Q22) MUTATED	93	29	48	83
AMP PEAK 5(1Q22) WILD-TYPE	126	29	89	33

Figure S57. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S58. Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 5(1Q22) MUTATED	89	42	62
AMP PEAK 5(1Q22) WILD-TYPE	55	73	77

Figure S58. Get High-res Image Gene #5: 'amp_1q22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'MRNA_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 0.036

Table S59. Gene #6: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 6(1Q44) MUTATED	10	11	4	2
AMP PEAK 6(1Q44) WILD-TYPE	4	6	8	8

Figure S59. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.043

Table S60. Gene #6: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 6(1Q44) MUTATED	9	5	5	5	3
AMP PEAK 6(1Q44) WILD-TYPE	5	4	2	2	13

Figure S60. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S61. Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 6(1Q44) MUTATED	83	92	10	9	24
AMP PEAK 6(1Q44) WILD-TYPE	86	213	9	0	13

Figure S61. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q44' versus 'METHLYATION_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.042

Table S62. Gene #6: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 6(1Q44) MUTATED	74	26	61
AMP PEAK 6(1Q44) WILD-TYPE	91	63	110

Figure S62. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q44' versus 'RPPA_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.027

Table S63. Gene #6: 'amp_1q44' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 6(1Q44) MUTATED	57	72	34	15
AMP PEAK 6(1Q44) WILD-TYPE	51	110	59	35

Figure S63. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.002

Table S64. Gene #6: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 6(1Q44) MUTATED	99	75	44
AMP PEAK 6(1Q44) WILD-TYPE	135	78	106

Figure S64. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.00096

Table S65. Gene #6: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 6(1Q44) MUTATED	61	29	16	34	37	21	20
AMP PEAK 6(1Q44) WILD-TYPE	62	24	31	31	71	45	55

Figure S65. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q44' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S66. Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 6(1Q44) MUTATED	87	85	44
AMP PEAK 6(1Q44) WILD-TYPE	136	65	113

Figure S66. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q44' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00603 (Fisher's exact test), Q value = 0.0074

Table S67. Gene #6: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 6(1Q44) MUTATED	85	30	43	58
AMP PEAK 6(1Q44) WILD-TYPE	134	28	94	58

Figure S67. Get High-res Image Gene #6: 'amp_1q44' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S68. Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 7(2P24.3) MUTATED	79	14	12	4	12
AMP PEAK 7(2P24.3) WILD-TYPE	90	291	7	5	25

Figure S68. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S69. Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 7(2P24.3) MUTATED	66	11	19
AMP PEAK 7(2P24.3) WILD-TYPE	99	78	152

Figure S69. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p24.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S70. Gene #7: 'amp_2p24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 7(2P24.3) MUTATED	14	30	56
AMP PEAK 7(2P24.3) WILD-TYPE	111	121	101

Figure S70. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2p24.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S71. Gene #7: 'amp_2p24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 7(2P24.3) MUTATED	12	61	18	9
AMP PEAK 7(2P24.3) WILD-TYPE	96	121	75	41

Figure S71. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2p24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S72. Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 7(2P24.3) MUTATED	85	19	17
AMP PEAK 7(2P24.3) WILD-TYPE	149	134	133

Figure S72. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S73. Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 7(2P24.3) MUTATED	59	7	14	6	19	10	6
AMP PEAK 7(2P24.3) WILD-TYPE	64	46	33	59	89	56	69

Figure S73. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S74. Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 7(2P24.3) MUTATED	79	21	19
AMP PEAK 7(2P24.3) WILD-TYPE	144	129	138

Figure S74. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S75. Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 7(2P24.3) MUTATED	39	7	18	55
AMP PEAK 7(2P24.3) WILD-TYPE	180	51	119	61

Figure S75. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00027

Table S76. Gene #7: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 7(2P24.3) MUTATED	56	20	16
AMP PEAK 7(2P24.3) WILD-TYPE	116	76	114

Figure S76. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 8e-04

Table S77. Gene #7: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 7(2P24.3) MUTATED	46	14	32
AMP PEAK 7(2P24.3) WILD-TYPE	98	101	107

Figure S77. Get High-res Image Gene #7: 'amp_2p24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q13' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.033

Table S78. Gene #8: 'amp_2q13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 8(2Q13) MUTATED	3	5	1	0	1
AMP PEAK 8(2Q13) WILD-TYPE	11	4	6	7	15

Figure S78. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S79. Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 8(2Q13) MUTATED	90	8	9	3	9
AMP PEAK 8(2Q13) WILD-TYPE	79	297	10	6	28

Figure S79. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S80. Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 8(2Q13) MUTATED	72	14	10
AMP PEAK 8(2Q13) WILD-TYPE	93	75	161

Figure S80. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q13' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S81. Gene #8: 'amp_2q13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 8(2Q13) MUTATED	13	29	57
AMP PEAK 8(2Q13) WILD-TYPE	112	122	100

Figure S81. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2q13' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S82. Gene #8: 'amp_2q13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 8(2Q13) MUTATED	9	61	19	10
AMP PEAK 8(2Q13) WILD-TYPE	99	121	74	40

Figure S82. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_2q13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S83. Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 8(2Q13) MUTATED	98	11	9
AMP PEAK 8(2Q13) WILD-TYPE	136	142	141

Figure S83. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S84. Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 8(2Q13) MUTATED	73	5	13	2	15	6	4
AMP PEAK 8(2Q13) WILD-TYPE	50	48	34	63	93	60	71

Figure S84. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S85. Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 8(2Q13) MUTATED	92	16	9
AMP PEAK 8(2Q13) WILD-TYPE	131	134	148

Figure S85. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S86. Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 8(2Q13) MUTATED	37	5	10	65
AMP PEAK 8(2Q13) WILD-TYPE	182	53	127	51

Figure S86. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2q13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S87. Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 8(2Q13) MUTATED	61	22	11
AMP PEAK 8(2Q13) WILD-TYPE	111	74	119

Figure S87. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2q13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S88. Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 8(2Q13) MUTATED	51	8	35
AMP PEAK 8(2Q13) WILD-TYPE	93	107	104

Figure S88. Get High-res Image Gene #8: 'amp_2q13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S89. Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 9(3P25.1) MUTATED	62	4	1	3	12
AMP PEAK 9(3P25.1) WILD-TYPE	107	301	18	6	25

Figure S89. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S90. Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 9(3P25.1) MUTATED	44	14	10
AMP PEAK 9(3P25.1) WILD-TYPE	121	75	161

Figure S90. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p25.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S91. Gene #9: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 9(3P25.1) MUTATED	10	12	41
AMP PEAK 9(3P25.1) WILD-TYPE	115	139	116

Figure S91. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3p25.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S92. Gene #9: 'amp_3p25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 9(3P25.1) MUTATED	6	44	9	4
AMP PEAK 9(3P25.1) WILD-TYPE	102	138	84	46

Figure S92. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S93. Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 9(3P25.1) MUTATED	66	4	12
AMP PEAK 9(3P25.1) WILD-TYPE	168	149	138

Figure S93. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S94. Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 9(3P25.1) MUTATED	41	0	13	4	15	5	4
AMP PEAK 9(3P25.1) WILD-TYPE	82	53	34	61	93	61	71

Figure S94. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S95. Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 9(3P25.1) MUTATED	58	11	11
AMP PEAK 9(3P25.1) WILD-TYPE	165	139	146

Figure S95. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S96. Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 9(3P25.1) MUTATED	24	0	13	43
AMP PEAK 9(3P25.1) WILD-TYPE	195	58	124	73

Figure S96. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S97. Gene #9: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 9(3P25.1) MUTATED	40	18	7
AMP PEAK 9(3P25.1) WILD-TYPE	132	78	123

Figure S97. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0019

Table S98. Gene #9: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 9(3P25.1) MUTATED	35	9	21
AMP PEAK 9(3P25.1) WILD-TYPE	109	106	118

Figure S98. Get High-res Image Gene #9: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3p14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S99. Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 10(3P14.1) MUTATED	46	3	1	3	12
AMP PEAK 10(3P14.1) WILD-TYPE	123	302	18	6	25

Figure S99. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p14.1' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00038

Table S100. Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 10(3P14.1) MUTATED	35	10	11
AMP PEAK 10(3P14.1) WILD-TYPE	130	79	160

Figure S100. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3p14.1' versus 'RPPA_CNMF'

P value = 0.00977 (Fisher's exact test), Q value = 0.012

Table S101. Gene #10: 'amp_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 10(3P14.1) MUTATED	8	13	27
AMP PEAK 10(3P14.1) WILD-TYPE	117	138	130

Figure S101. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3p14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.0186 (Fisher's exact test), Q value = 0.022

Table S102. Gene #10: 'amp_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 10(3P14.1) MUTATED	5	28	12	3
AMP PEAK 10(3P14.1) WILD-TYPE	103	154	81	47

Figure S102. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3p14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S103. Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 10(3P14.1) MUTATED	49	4	12
AMP PEAK 10(3P14.1) WILD-TYPE	185	149	138

Figure S103. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S104. Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 10(3P14.1) MUTATED	29	0	9	4	14	4	5
AMP PEAK 10(3P14.1) WILD-TYPE	94	53	38	61	94	62	70

Figure S104. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S105. Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 10(3P14.1) MUTATED	44	10	10
AMP PEAK 10(3P14.1) WILD-TYPE	179	140	147

Figure S105. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S106. Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 10(3P14.1) MUTATED	20	0	13	31
AMP PEAK 10(3P14.1) WILD-TYPE	199	58	124	85

Figure S106. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00321 (Fisher's exact test), Q value = 0.004

Table S107. Gene #10: 'amp_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 10(3P14.1) MUTATED	28	17	7
AMP PEAK 10(3P14.1) WILD-TYPE	144	79	123

Figure S107. Get High-res Image Gene #10: 'amp_3p14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S108. Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 11(3Q26.2) MUTATED	1	11	1	0
AMP PEAK 11(3Q26.2) WILD-TYPE	13	6	11	10

Figure S108. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S109. Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 11(3Q26.2) MUTATED	4	8	1	0	0
AMP PEAK 11(3Q26.2) WILD-TYPE	10	1	6	7	16

Figure S109. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S110. Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 11(3Q26.2) MUTATED	141	11	3	5	15
AMP PEAK 11(3Q26.2) WILD-TYPE	28	294	16	4	22

Figure S110. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S111. Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 11(3Q26.2) MUTATED	102	25	23
AMP PEAK 11(3Q26.2) WILD-TYPE	63	64	148

Figure S111. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S112. Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 11(3Q26.2) MUTATED	19	34	81
AMP PEAK 11(3Q26.2) WILD-TYPE	106	117	76

Figure S112. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S113. Gene #11: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 11(3Q26.2) MUTATED	10	80	32	12
AMP PEAK 11(3Q26.2) WILD-TYPE	98	102	61	38

Figure S113. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S114. Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 11(3Q26.2) MUTATED	143	7	24
AMP PEAK 11(3Q26.2) WILD-TYPE	91	146	126

Figure S114. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S115. Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 11(3Q26.2) MUTATED	95	0	26	5	26	14	8
AMP PEAK 11(3Q26.2) WILD-TYPE	28	53	21	60	82	52	67

Figure S115. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S116. Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 11(3Q26.2) MUTATED	131	19	21
AMP PEAK 11(3Q26.2) WILD-TYPE	92	131	136

Figure S116. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S117. Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 11(3Q26.2) MUTATED	61	0	24	86
AMP PEAK 11(3Q26.2) WILD-TYPE	158	58	113	30

Figure S117. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S118. Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 11(3Q26.2) MUTATED	85	33	25
AMP PEAK 11(3Q26.2) WILD-TYPE	87	63	105

Figure S118. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S119. Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 11(3Q26.2) MUTATED	78	20	45
AMP PEAK 11(3Q26.2) WILD-TYPE	66	95	94

Figure S119. Get High-res Image Gene #11: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 4e-04

Table S120. Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 12(3Q26.2) MUTATED	1	10	1	0
AMP PEAK 12(3Q26.2) WILD-TYPE	13	7	11	10

Figure S120. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S121. Gene #12: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 12(3Q26.2) MUTATED	3	8	1	0	0
AMP PEAK 12(3Q26.2) WILD-TYPE	11	1	6	7	16

Figure S121. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S122. Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 12(3Q26.2) MUTATED	135	7	3	5	14
AMP PEAK 12(3Q26.2) WILD-TYPE	34	298	16	4	23

Figure S122. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S123. Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 12(3Q26.2) MUTATED	101	20	20
AMP PEAK 12(3Q26.2) WILD-TYPE	64	69	151

Figure S123. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S124. Gene #12: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 12(3Q26.2) MUTATED	17	32	79
AMP PEAK 12(3Q26.2) WILD-TYPE	108	119	78

Figure S124. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S125. Gene #12: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 12(3Q26.2) MUTATED	8	77	30	13
AMP PEAK 12(3Q26.2) WILD-TYPE	100	105	63	37

Figure S125. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S126. Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 12(3Q26.2) MUTATED	136	7	20
AMP PEAK 12(3Q26.2) WILD-TYPE	98	146	130

Figure S126. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S127. Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 12(3Q26.2) MUTATED	92	0	24	5	24	11	7
AMP PEAK 12(3Q26.2) WILD-TYPE	31	53	23	60	84	55	68

Figure S127. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S128. Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 12(3Q26.2) MUTATED	123	19	18
AMP PEAK 12(3Q26.2) WILD-TYPE	100	131	139

Figure S128. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S129. Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 12(3Q26.2) MUTATED	57	0	20	83
AMP PEAK 12(3Q26.2) WILD-TYPE	162	58	117	33

Figure S129. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S130. Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 12(3Q26.2) MUTATED	84	28	22
AMP PEAK 12(3Q26.2) WILD-TYPE	88	68	108

Figure S130. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S131. Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 12(3Q26.2) MUTATED	77	16	41
AMP PEAK 12(3Q26.2) WILD-TYPE	67	99	98

Figure S131. Get High-res Image Gene #12: 'amp_3q26.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.009

Table S132. Gene #13: 'amp_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 13(4P16.3) MUTATED	2	4	0	0	0
AMP PEAK 13(4P16.3) WILD-TYPE	12	5	7	7	16

Figure S132. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S133. Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 13(4P16.3) MUTATED	50	2	0	0	1
AMP PEAK 13(4P16.3) WILD-TYPE	119	303	19	9	36

Figure S133. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4p16.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S134. Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 13(4P16.3) MUTATED	30	8	6
AMP PEAK 13(4P16.3) WILD-TYPE	135	81	165

Figure S134. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4p16.3' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S135. Gene #13: 'amp_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 13(4P16.3) MUTATED	6	6	29
AMP PEAK 13(4P16.3) WILD-TYPE	119	145	128

Figure S135. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S136. Gene #13: 'amp_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 13(4P16.3) MUTATED	1	30	9	1
AMP PEAK 13(4P16.3) WILD-TYPE	107	152	84	49

Figure S136. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S137. Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 13(4P16.3) MUTATED	49	1	2
AMP PEAK 13(4P16.3) WILD-TYPE	185	152	148

Figure S137. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S138. Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 13(4P16.3) MUTATED	39	0	3	0	8	1	1
AMP PEAK 13(4P16.3) WILD-TYPE	84	53	44	65	100	65	74

Figure S138. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S139. Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 13(4P16.3) MUTATED	44	3	4
AMP PEAK 13(4P16.3) WILD-TYPE	179	147	153

Figure S139. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S140. Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 13(4P16.3) MUTATED	13	0	4	34
AMP PEAK 13(4P16.3) WILD-TYPE	206	58	133	82

Figure S140. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.0017

Table S141. Gene #13: 'amp_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 13(4P16.3) MUTATED	29	7	6
AMP PEAK 13(4P16.3) WILD-TYPE	143	89	124

Figure S141. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00056

Table S142. Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 13(4P16.3) MUTATED	26	4	12
AMP PEAK 13(4P16.3) WILD-TYPE	118	111	127

Figure S142. Get High-res Image Gene #13: 'amp_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.049

Table S143. Gene #14: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 14(5P15.33) MUTATED	2	4	1	1	0
AMP PEAK 14(5P15.33) WILD-TYPE	12	5	6	6	16

Figure S143. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S144. Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 14(5P15.33) MUTATED	80	4	4	1	0
AMP PEAK 14(5P15.33) WILD-TYPE	89	301	15	8	37

Figure S144. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S145. Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 14(5P15.33) MUTATED	58	11	7
AMP PEAK 14(5P15.33) WILD-TYPE	107	78	164

Figure S145. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S146. Gene #14: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 14(5P15.33) MUTATED	9	17	48
AMP PEAK 14(5P15.33) WILD-TYPE	116	134	109

Figure S146. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5p15.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S147. Gene #14: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 14(5P15.33) MUTATED	5	50	15	4
AMP PEAK 14(5P15.33) WILD-TYPE	103	132	78	46

Figure S147. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S148. Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 14(5P15.33) MUTATED	79	5	4
AMP PEAK 14(5P15.33) WILD-TYPE	155	148	146

Figure S148. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S149. Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 14(5P15.33) MUTATED	54	3	13	2	11	5	0
AMP PEAK 14(5P15.33) WILD-TYPE	69	50	34	63	97	61	75

Figure S149. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S150. Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 14(5P15.33) MUTATED	71	12	5
AMP PEAK 14(5P15.33) WILD-TYPE	152	138	152

Figure S150. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S151. Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 14(5P15.33) MUTATED	28	3	5	52
AMP PEAK 14(5P15.33) WILD-TYPE	191	55	132	64

Figure S151. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S152. Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 14(5P15.33) MUTATED	54	15	6
AMP PEAK 14(5P15.33) WILD-TYPE	118	81	124

Figure S152. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S153. Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 14(5P15.33) MUTATED	47	4	24
AMP PEAK 14(5P15.33) WILD-TYPE	97	111	115

Figure S153. Get High-res Image Gene #14: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5q35.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S154. Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 15(5Q35.3) MUTATED	51	1	4	1	0
AMP PEAK 15(5Q35.3) WILD-TYPE	118	304	15	8	37

Figure S154. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S155. Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 15(5Q35.3) MUTATED	35	9	6
AMP PEAK 15(5Q35.3) WILD-TYPE	130	80	165

Figure S155. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5q35.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S156. Gene #15: 'amp_5q35.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 15(5Q35.3) MUTATED	6	7	33
AMP PEAK 15(5Q35.3) WILD-TYPE	119	144	124

Figure S156. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_5q35.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00034

Table S157. Gene #15: 'amp_5q35.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 15(5Q35.3) MUTATED	4	33	7	2
AMP PEAK 15(5Q35.3) WILD-TYPE	104	149	86	48

Figure S157. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_5q35.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S158. Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 15(5Q35.3) MUTATED	50	4	3
AMP PEAK 15(5Q35.3) WILD-TYPE	184	149	147

Figure S158. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_5q35.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S159. Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 15(5Q35.3) MUTATED	35	2	9	1	7	2	1
AMP PEAK 15(5Q35.3) WILD-TYPE	88	51	38	64	101	64	74

Figure S159. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S160. Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 15(5Q35.3) MUTATED	44	8	4
AMP PEAK 15(5Q35.3) WILD-TYPE	179	142	153

Figure S160. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5q35.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S161. Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 15(5Q35.3) MUTATED	18	3	4	31
AMP PEAK 15(5Q35.3) WILD-TYPE	201	55	133	85

Figure S161. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.00081

Table S162. Gene #15: 'amp_5q35.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 15(5Q35.3) MUTATED	30	13	5
AMP PEAK 15(5Q35.3) WILD-TYPE	142	83	125

Figure S162. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5q35.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0016

Table S163. Gene #15: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 15(5Q35.3) MUTATED	27	5	16
AMP PEAK 15(5Q35.3) WILD-TYPE	117	110	123

Figure S163. Get High-res Image Gene #15: 'amp_5q35.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p24.2' versus 'MRNA_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.0039

Table S164. Gene #16: 'amp_6p24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 16(6P24.2) MUTATED	1	9	2	0
AMP PEAK 16(6P24.2) WILD-TYPE	13	8	10	10

Figure S164. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p24.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.00069

Table S165. Gene #16: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 16(6P24.2) MUTATED	3	7	0	0	2
AMP PEAK 16(6P24.2) WILD-TYPE	11	2	7	7	14

Figure S165. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S166. Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 16(6P24.2) MUTATED	95	8	1	1	12
AMP PEAK 16(6P24.2) WILD-TYPE	74	297	18	8	25

Figure S166. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S167. Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 16(6P24.2) MUTATED	73	15	12
AMP PEAK 16(6P24.2) WILD-TYPE	92	74	159

Figure S167. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p24.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S168. Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 16(6P24.2) MUTATED	8	15	63
AMP PEAK 16(6P24.2) WILD-TYPE	117	136	94

Figure S168. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p24.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S169. Gene #16: 'amp_6p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 16(6P24.2) MUTATED	5	57	18	6
AMP PEAK 16(6P24.2) WILD-TYPE	103	125	75	44

Figure S169. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S170. Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 16(6P24.2) MUTATED	97	5	15
AMP PEAK 16(6P24.2) WILD-TYPE	137	148	135

Figure S170. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S171. Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 16(6P24.2) MUTATED	68	0	11	5	19	8	6
AMP PEAK 16(6P24.2) WILD-TYPE	55	53	36	60	89	58	69

Figure S171. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S172. Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 16(6P24.2) MUTATED	84	18	12
AMP PEAK 16(6P24.2) WILD-TYPE	139	132	145

Figure S172. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S173. Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 16(6P24.2) MUTATED	42	0	12	60
AMP PEAK 16(6P24.2) WILD-TYPE	177	58	125	56

Figure S173. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S174. Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 16(6P24.2) MUTATED	58	24	14
AMP PEAK 16(6P24.2) WILD-TYPE	114	72	116

Figure S174. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S175. Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 16(6P24.2) MUTATED	51	13	32
AMP PEAK 16(6P24.2) WILD-TYPE	93	102	107

Figure S175. Get High-res Image Gene #16: 'amp_6p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S176. Gene #17: 'amp_6p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 17(6P22.3) MUTATED	86	7	1	1	12
AMP PEAK 17(6P22.3) WILD-TYPE	83	298	18	8	25

Figure S176. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S177. Gene #17: 'amp_6p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 17(6P22.3) MUTATED	70	15	10
AMP PEAK 17(6P22.3) WILD-TYPE	95	74	161

Figure S177. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p22.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S178. Gene #17: 'amp_6p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 17(6P22.3) MUTATED	9	13	58
AMP PEAK 17(6P22.3) WILD-TYPE	116	138	99

Figure S178. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S179. Gene #17: 'amp_6p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 17(6P22.3) MUTATED	4	53	18	5
AMP PEAK 17(6P22.3) WILD-TYPE	104	129	75	45

Figure S179. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S180. Gene #17: 'amp_6p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 17(6P22.3) MUTATED	88	5	14
AMP PEAK 17(6P22.3) WILD-TYPE	146	148	136

Figure S180. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S181. Gene #17: 'amp_6p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 17(6P22.3) MUTATED	61	0	12	5	16	7	6
AMP PEAK 17(6P22.3) WILD-TYPE	62	53	35	60	92	59	69

Figure S181. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S182. Gene #17: 'amp_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 17(6P22.3) MUTATED	80	15	11
AMP PEAK 17(6P22.3) WILD-TYPE	143	135	146

Figure S182. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S183. Gene #17: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 17(6P22.3) MUTATED	39	0	11	56
AMP PEAK 17(6P22.3) WILD-TYPE	180	58	126	60

Figure S183. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S184. Gene #17: 'amp_6p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 17(6P22.3) MUTATED	58	21	12
AMP PEAK 17(6P22.3) WILD-TYPE	114	75	118

Figure S184. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S185. Gene #17: 'amp_6p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 17(6P22.3) MUTATED	50	11	30
AMP PEAK 17(6P22.3) WILD-TYPE	94	104	109

Figure S185. Get High-res Image Gene #17: 'amp_6p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S186. Gene #18: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 18(6Q25.1) MUTATED	65	7	3	2	11
AMP PEAK 18(6Q25.1) WILD-TYPE	104	298	16	7	26

Figure S186. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S187. Gene #18: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 18(6Q25.1) MUTATED	55	10	14
AMP PEAK 18(6Q25.1) WILD-TYPE	110	79	157

Figure S187. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q25.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S188. Gene #18: 'amp_6q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 18(6Q25.1) MUTATED	4	16	47
AMP PEAK 18(6Q25.1) WILD-TYPE	121	135	110

Figure S188. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S189. Gene #18: 'amp_6q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 18(6Q25.1) MUTATED	4	41	17	5
AMP PEAK 18(6Q25.1) WILD-TYPE	104	141	76	45

Figure S189. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S190. Gene #18: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 18(6Q25.1) MUTATED	63	7	17
AMP PEAK 18(6Q25.1) WILD-TYPE	171	146	133

Figure S190. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S191. Gene #18: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 18(6Q25.1) MUTATED	40	0	9	6	15	11	6
AMP PEAK 18(6Q25.1) WILD-TYPE	83	53	38	59	93	55	69

Figure S191. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S192. Gene #18: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 18(6Q25.1) MUTATED	57	19	12
AMP PEAK 18(6Q25.1) WILD-TYPE	166	131	145

Figure S192. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S193. Gene #18: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 18(6Q25.1) MUTATED	39	1	12	36
AMP PEAK 18(6Q25.1) WILD-TYPE	180	57	125	80

Figure S193. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S194. Gene #18: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 18(6Q25.1) MUTATED	48	17	11
AMP PEAK 18(6Q25.1) WILD-TYPE	124	79	119

Figure S194. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.035

Table S195. Gene #18: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 18(6Q25.1) MUTATED	37	15	24
AMP PEAK 18(6Q25.1) WILD-TYPE	107	100	115

Figure S195. Get High-res Image Gene #18: 'amp_6q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S196. Gene #19: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 19(7Q31.2) MUTATED	53	15	13	2	10
AMP PEAK 19(7Q31.2) WILD-TYPE	116	290	6	7	27

Figure S196. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q31.2' versus 'METHLYATION_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S197. Gene #19: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 19(7Q31.2) MUTATED	45	8	21
AMP PEAK 19(7Q31.2) WILD-TYPE	120	81	150

Figure S197. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q31.2' versus 'RPPA_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.0034

Table S198. Gene #19: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 19(7Q31.2) MUTATED	12	20	38
AMP PEAK 19(7Q31.2) WILD-TYPE	113	131	119

Figure S198. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_7q31.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0014

Table S199. Gene #19: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 19(7Q31.2) MUTATED	8	44	12	6
AMP PEAK 19(7Q31.2) WILD-TYPE	100	138	81	44

Figure S199. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_7q31.2' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00041

Table S200. Gene #19: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 19(7Q31.2) MUTATED	58	17	18
AMP PEAK 19(7Q31.2) WILD-TYPE	176	136	132

Figure S200. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S201. Gene #19: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 19(7Q31.2) MUTATED	34	8	13	2	19	10	7
AMP PEAK 19(7Q31.2) WILD-TYPE	89	45	34	63	89	56	68

Figure S201. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00119 (Fisher's exact test), Q value = 0.0016

Table S202. Gene #19: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 19(7Q31.2) MUTATED	54	23	16
AMP PEAK 19(7Q31.2) WILD-TYPE	169	127	141

Figure S202. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q31.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 0.013

Table S203. Gene #19: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 19(7Q31.2) MUTATED	35	10	16	32
AMP PEAK 19(7Q31.2) WILD-TYPE	184	48	121	84

Figure S203. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.024

Table S204. Gene #19: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 19(7Q31.2) MUTATED	39	19	14
AMP PEAK 19(7Q31.2) WILD-TYPE	133	77	116

Figure S204. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q31.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0145 (Fisher's exact test), Q value = 0.017

Table S205. Gene #19: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 19(7Q31.2) MUTATED	35	12	25
AMP PEAK 19(7Q31.2) WILD-TYPE	109	103	114

Figure S205. Get High-res Image Gene #19: 'amp_7q31.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S206. Gene #20: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 20(8P11.22) MUTATED	50	29	8	2	37
AMP PEAK 20(8P11.22) WILD-TYPE	119	276	11	7	0

Figure S206. Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S207. Gene #20: 'amp_8p11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 20(8P11.22) MUTATED	15	37	37	13
AMP PEAK 20(8P11.22) WILD-TYPE	93	145	56	37

Figure S207. Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00806 (Fisher's exact test), Q value = 0.0097

Table S208. Gene #20: 'amp_8p11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 20(8P11.22) MUTATED	30	9	9	9	36	22	11
AMP PEAK 20(8P11.22) WILD-TYPE	93	44	38	56	72	44	64

Figure S208. Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0364 (Fisher's exact test), Q value = 0.041

Table S209. Gene #20: 'amp_8p11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 20(8P11.22) MUTATED	61	6	32	25
AMP PEAK 20(8P11.22) WILD-TYPE	158	52	105	91

Figure S209. Get High-res Image Gene #20: 'amp_8p11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.012

Table S210. Gene #21: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 21(8P11.21) MUTATED	1	8	2	0
AMP PEAK 21(8P11.21) WILD-TYPE	13	9	10	10

Figure S210. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.035

Table S211. Gene #21: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 21(8P11.21) MUTATED	4	5	0	0	2
AMP PEAK 21(8P11.21) WILD-TYPE	10	4	7	7	14

Figure S211. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S212. Gene #21: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 21(8P11.21) MUTATED	87	29	8	2	36
AMP PEAK 21(8P11.21) WILD-TYPE	82	276	11	7	1

Figure S212. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 0.00311 (Fisher's exact test), Q value = 0.0039

Table S213. Gene #21: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 21(8P11.21) MUTATED	69	27	42
AMP PEAK 21(8P11.21) WILD-TYPE	96	62	129

Figure S213. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00041

Table S214. Gene #21: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 21(8P11.21) MUTATED	27	37	65
AMP PEAK 21(8P11.21) WILD-TYPE	98	114	92

Figure S214. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S215. Gene #21: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 21(8P11.21) MUTATED	15	58	39	17
AMP PEAK 21(8P11.21) WILD-TYPE	93	124	54	33

Figure S215. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S216. Gene #21: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 21(8P11.21) MUTATED	100	29	33
AMP PEAK 21(8P11.21) WILD-TYPE	134	124	117

Figure S216. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S217. Gene #21: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 21(8P11.21) MUTATED	59	9	19	10	34	20	11
AMP PEAK 21(8P11.21) WILD-TYPE	64	44	28	55	74	46	64

Figure S217. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S218. Gene #21: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 21(8P11.21) MUTATED	91	35	33
AMP PEAK 21(8P11.21) WILD-TYPE	132	115	124

Figure S218. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S219. Gene #21: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 21(8P11.21) MUTATED	62	6	31	60
AMP PEAK 21(8P11.21) WILD-TYPE	157	52	106	56

Figure S219. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S220. Gene #21: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 21(8P11.21) MUTATED	75	30	26
AMP PEAK 21(8P11.21) WILD-TYPE	97	66	104

Figure S220. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00177 (Fisher's exact test), Q value = 0.0023

Table S221. Gene #21: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 21(8P11.21) MUTATED	62	26	43
AMP PEAK 21(8P11.21) WILD-TYPE	82	89	96

Figure S221. Get High-res Image Gene #21: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.014

Table S222. Gene #22: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 22(8Q24.21) MUTATED	1	8	3	0
AMP PEAK 22(8Q24.21) WILD-TYPE	13	9	9	10

Figure S222. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S223. Gene #22: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 22(8Q24.21) MUTATED	126	35	8	3	37
AMP PEAK 22(8Q24.21) WILD-TYPE	43	270	11	6	0

Figure S223. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S224. Gene #22: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 22(8Q24.21) MUTATED	101	32	48
AMP PEAK 22(8Q24.21) WILD-TYPE	64	57	123

Figure S224. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S225. Gene #22: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 22(8Q24.21) MUTATED	30	47	86
AMP PEAK 22(8Q24.21) WILD-TYPE	95	104	71

Figure S225. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S226. Gene #22: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 22(8Q24.21) MUTATED	16	82	44	21
AMP PEAK 22(8Q24.21) WILD-TYPE	92	100	49	29

Figure S226. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S227. Gene #22: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 22(8Q24.21) MUTATED	140	29	39
AMP PEAK 22(8Q24.21) WILD-TYPE	94	124	111

Figure S227. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S228. Gene #22: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 22(8Q24.21) MUTATED	86	10	27	8	39	26	12
AMP PEAK 22(8Q24.21) WILD-TYPE	37	43	20	57	69	40	63

Figure S228. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S229. Gene #22: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 22(8Q24.21) MUTATED	130	38	38
AMP PEAK 22(8Q24.21) WILD-TYPE	93	112	119

Figure S229. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S230. Gene #22: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 22(8Q24.21) MUTATED	83	6	35	82
AMP PEAK 22(8Q24.21) WILD-TYPE	136	52	102	34

Figure S230. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S231. Gene #22: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 22(8Q24.21) MUTATED	95	41	33
AMP PEAK 22(8Q24.21) WILD-TYPE	77	55	97

Figure S231. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S232. Gene #22: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 22(8Q24.21) MUTATED	83	30	56
AMP PEAK 22(8Q24.21) WILD-TYPE	61	85	83

Figure S232. Get High-res Image Gene #22: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0035

Table S233. Gene #23: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 23(8Q24.21) MUTATED	1	9	2	0
AMP PEAK 23(8Q24.21) WILD-TYPE	13	8	10	10

Figure S233. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00605 (Fisher's exact test), Q value = 0.0074

Table S234. Gene #23: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 23(8Q24.21) MUTATED	4	6	0	0	2
AMP PEAK 23(8Q24.21) WILD-TYPE	10	3	7	7	14

Figure S234. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S235. Gene #23: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 23(8Q24.21) MUTATED	127	40	8	3	37
AMP PEAK 23(8Q24.21) WILD-TYPE	42	265	11	6	0

Figure S235. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S236. Gene #23: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 23(8Q24.21) MUTATED	101	31	53
AMP PEAK 23(8Q24.21) WILD-TYPE	64	58	118

Figure S236. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S237. Gene #23: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 23(8Q24.21) MUTATED	35	49	86
AMP PEAK 23(8Q24.21) WILD-TYPE	90	102	71

Figure S237. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S238. Gene #23: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 23(8Q24.21) MUTATED	16	85	45	24
AMP PEAK 23(8Q24.21) WILD-TYPE	92	97	48	26

Figure S238. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S239. Gene #23: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 23(8Q24.21) MUTATED	142	32	40
AMP PEAK 23(8Q24.21) WILD-TYPE	92	121	110

Figure S239. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S240. Gene #23: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 23(8Q24.21) MUTATED	91	11	25	9	39	25	14
AMP PEAK 23(8Q24.21) WILD-TYPE	32	42	22	56	69	41	61

Figure S240. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S241. Gene #23: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 23(8Q24.21) MUTATED	135	38	38
AMP PEAK 23(8Q24.21) WILD-TYPE	88	112	119

Figure S241. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S242. Gene #23: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 23(8Q24.21) MUTATED	83	7	38	83
AMP PEAK 23(8Q24.21) WILD-TYPE	136	51	99	33

Figure S242. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S243. Gene #23: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 23(8Q24.21) MUTATED	98	40	36
AMP PEAK 23(8Q24.21) WILD-TYPE	74	56	94

Figure S243. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S244. Gene #23: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 23(8Q24.21) MUTATED	88	32	54
AMP PEAK 23(8Q24.21) WILD-TYPE	56	83	85

Figure S244. Get High-res Image Gene #23: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9p24.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S245. Gene #24: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 24(9P24.2) MUTATED	59	4	1	0	1
AMP PEAK 24(9P24.2) WILD-TYPE	110	301	18	9	36

Figure S245. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p24.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S246. Gene #24: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 24(9P24.2) MUTATED	42	7	5
AMP PEAK 24(9P24.2) WILD-TYPE	123	82	166

Figure S246. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p24.2' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S247. Gene #24: 'amp_9p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 24(9P24.2) MUTATED	5	16	34
AMP PEAK 24(9P24.2) WILD-TYPE	120	135	123

Figure S247. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9p24.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S248. Gene #24: 'amp_9p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 24(9P24.2) MUTATED	1	38	15	1
AMP PEAK 24(9P24.2) WILD-TYPE	107	144	78	49

Figure S248. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9p24.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S249. Gene #24: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 24(9P24.2) MUTATED	57	3	5
AMP PEAK 24(9P24.2) WILD-TYPE	177	150	145

Figure S249. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S250. Gene #24: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 24(9P24.2) MUTATED	41	0	6	2	12	4	0
AMP PEAK 24(9P24.2) WILD-TYPE	82	53	41	63	96	62	75

Figure S250. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S251. Gene #24: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 24(9P24.2) MUTATED	54	8	2
AMP PEAK 24(9P24.2) WILD-TYPE	169	142	155

Figure S251. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p24.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S252. Gene #24: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 24(9P24.2) MUTATED	21	2	3	38
AMP PEAK 24(9P24.2) WILD-TYPE	198	56	134	78

Figure S252. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00028

Table S253. Gene #24: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 24(9P24.2) MUTATED	35	11	6
AMP PEAK 24(9P24.2) WILD-TYPE	137	85	124

Figure S253. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9p24.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 3e-04

Table S254. Gene #24: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 24(9P24.2) MUTATED	31	5	16
AMP PEAK 24(9P24.2) WILD-TYPE	113	110	123

Figure S254. Get High-res Image Gene #24: 'amp_9p24.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.017

Table S255. Gene #25: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 25(9Q34.3) MUTATED	0	4	1	0	1
AMP PEAK 25(9Q34.3) WILD-TYPE	14	5	6	7	15

Figure S255. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_9q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S256. Gene #25: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 25(9Q34.3) MUTATED	35	2	0	1	1
AMP PEAK 25(9Q34.3) WILD-TYPE	134	303	19	8	36

Figure S256. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9q34.3' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S257. Gene #25: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 25(9Q34.3) MUTATED	22	6	2
AMP PEAK 25(9Q34.3) WILD-TYPE	143	83	169

Figure S257. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9q34.3' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0016

Table S258. Gene #25: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 25(9Q34.3) MUTATED	3	8	21
AMP PEAK 25(9Q34.3) WILD-TYPE	122	143	136

Figure S258. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00207 (Fisher's exact test), Q value = 0.0026

Table S259. Gene #25: 'amp_9q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 25(9Q34.3) MUTATED	1	22	6	3
AMP PEAK 25(9Q34.3) WILD-TYPE	107	160	87	47

Figure S259. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S260. Gene #25: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 25(9Q34.3) MUTATED	34	3	1
AMP PEAK 25(9Q34.3) WILD-TYPE	200	150	149

Figure S260. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S261. Gene #25: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 25(9Q34.3) MUTATED	30	2	2	0	2	2	0
AMP PEAK 25(9Q34.3) WILD-TYPE	93	51	45	65	106	64	75

Figure S261. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S262. Gene #25: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 25(9Q34.3) MUTATED	28	4	3
AMP PEAK 25(9Q34.3) WILD-TYPE	195	146	154

Figure S262. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S263. Gene #25: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 25(9Q34.3) MUTATED	10	1	2	22
AMP PEAK 25(9Q34.3) WILD-TYPE	209	57	135	94

Figure S263. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0437 (Fisher's exact test), Q value = 0.049

Table S264. Gene #25: 'amp_9q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 25(9Q34.3) MUTATED	16	10	4
AMP PEAK 25(9Q34.3) WILD-TYPE	156	86	126

Figure S264. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_9q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0037

Table S265. Gene #25: 'amp_9q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 25(9Q34.3) MUTATED	18	2	10
AMP PEAK 25(9Q34.3) WILD-TYPE	126	113	129

Figure S265. Get High-res Image Gene #25: 'amp_9q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.2' versus 'MRNA_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.037

Table S266. Gene #26: 'amp_10q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 26(10Q22.2) MUTATED	2	7	8	2
AMP PEAK 26(10Q22.2) WILD-TYPE	12	10	4	8

Figure S266. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S267. Gene #26: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 26(10Q22.2) MUTATED	66	45	8	4	20
AMP PEAK 26(10Q22.2) WILD-TYPE	103	260	11	5	17

Figure S267. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10q22.2' versus 'RPPA_CNMF'

P value = 0.00367 (Fisher's exact test), Q value = 0.0045

Table S268. Gene #26: 'amp_10q22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 26(10Q22.2) MUTATED	27	33	58
AMP PEAK 26(10Q22.2) WILD-TYPE	98	118	99

Figure S268. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.016

Table S269. Gene #26: 'amp_10q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 26(10Q22.2) MUTATED	74	28	40
AMP PEAK 26(10Q22.2) WILD-TYPE	160	125	110

Figure S269. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00248 (Fisher's exact test), Q value = 0.0031

Table S270. Gene #26: 'amp_10q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 26(10Q22.2) MUTATED	49	15	10	10	22	21	15
AMP PEAK 26(10Q22.2) WILD-TYPE	74	38	37	55	86	45	60

Figure S270. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 0.015

Table S271. Gene #26: 'amp_10q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 26(10Q22.2) MUTATED	43	19	39	40
AMP PEAK 26(10Q22.2) WILD-TYPE	176	39	98	76

Figure S271. Get High-res Image Gene #26: 'amp_10q22.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNA_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0027

Table S272. Gene #27: 'amp_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 27(11P11.2) MUTATED	0	6	0	0
AMP PEAK 27(11P11.2) WILD-TYPE	14	11	12	10

Figure S272. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00814 (Fisher's exact test), Q value = 0.0098

Table S273. Gene #27: 'amp_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 27(11P11.2) MUTATED	2	4	0	0	0
AMP PEAK 27(11P11.2) WILD-TYPE	12	5	7	7	16

Figure S273. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S274. Gene #27: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 27(11P11.2) MUTATED	43	1	4	0	3
AMP PEAK 27(11P11.2) WILD-TYPE	126	304	15	9	34

Figure S274. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S275. Gene #27: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 27(11P11.2) MUTATED	30	9	4
AMP PEAK 27(11P11.2) WILD-TYPE	135	80	167

Figure S275. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11p11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S276. Gene #27: 'amp_11p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 27(11P11.2) MUTATED	5	8	30
AMP PEAK 27(11P11.2) WILD-TYPE	120	143	127

Figure S276. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00867 (Fisher's exact test), Q value = 0.01

Table S277. Gene #27: 'amp_11p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 27(11P11.2) MUTATED	3	26	10	4
AMP PEAK 27(11P11.2) WILD-TYPE	105	156	83	46

Figure S277. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S278. Gene #27: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 27(11P11.2) MUTATED	42	3	6
AMP PEAK 27(11P11.2) WILD-TYPE	192	150	144

Figure S278. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S279. Gene #27: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 27(11P11.2) MUTATED	35	1	2	2	6	4	1
AMP PEAK 27(11P11.2) WILD-TYPE	88	52	45	63	102	62	74

Figure S279. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S280. Gene #27: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 27(11P11.2) MUTATED	40	4	6
AMP PEAK 27(11P11.2) WILD-TYPE	183	146	151

Figure S280. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S281. Gene #27: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 27(11P11.2) MUTATED	14	1	4	31
AMP PEAK 27(11P11.2) WILD-TYPE	205	57	133	85

Figure S281. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.027

Table S282. Gene #27: 'amp_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 27(11P11.2) MUTATED	24	10	6
AMP PEAK 27(11P11.2) WILD-TYPE	148	86	124

Figure S282. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0407 (Fisher's exact test), Q value = 0.046

Table S283. Gene #27: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 27(11P11.2) MUTATED	18	5	17
AMP PEAK 27(11P11.2) WILD-TYPE	126	110	122

Figure S283. Get High-res Image Gene #27: 'amp_11p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.2' versus 'MRNA_CNMF'

P value = 0.00191 (Fisher's exact test), Q value = 0.0024

Table S284. Gene #28: 'amp_11q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 28(11Q13.2) MUTATED	0	6	0	0
AMP PEAK 28(11Q13.2) WILD-TYPE	14	11	12	10

Figure S284. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.0095

Table S285. Gene #28: 'amp_11q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 28(11Q13.2) MUTATED	2	4	0	0	0
AMP PEAK 28(11Q13.2) WILD-TYPE	12	5	7	7	16

Figure S285. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S286. Gene #28: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 28(11Q13.2) MUTATED	59	5	5	0	5
AMP PEAK 28(11Q13.2) WILD-TYPE	110	300	14	9	32

Figure S286. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S287. Gene #28: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 28(11Q13.2) MUTATED	43	8	12
AMP PEAK 28(11Q13.2) WILD-TYPE	122	81	159

Figure S287. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S288. Gene #28: 'amp_11q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 28(11Q13.2) MUTATED	6	18	39
AMP PEAK 28(11Q13.2) WILD-TYPE	119	133	118

Figure S288. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.00062

Table S289. Gene #28: 'amp_11q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 28(11Q13.2) MUTATED	5	40	12	6
AMP PEAK 28(11Q13.2) WILD-TYPE	103	142	81	44

Figure S289. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S290. Gene #28: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 28(11Q13.2) MUTATED	53	5	15
AMP PEAK 28(11Q13.2) WILD-TYPE	181	148	135

Figure S290. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S291. Gene #28: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 28(11Q13.2) MUTATED	39	1	2	2	16	10	3
AMP PEAK 28(11Q13.2) WILD-TYPE	84	52	45	63	92	56	72

Figure S291. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S292. Gene #28: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 28(11Q13.2) MUTATED	48	9	15
AMP PEAK 28(11Q13.2) WILD-TYPE	175	141	142

Figure S292. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S293. Gene #28: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 28(11Q13.2) MUTATED	28	1	12	31
AMP PEAK 28(11Q13.2) WILD-TYPE	191	57	125	85

Figure S293. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0089 (Fisher's exact test), Q value = 0.011

Table S294. Gene #28: 'amp_11q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 28(11Q13.2) MUTATED	32	13	14
AMP PEAK 28(11Q13.2) WILD-TYPE	112	102	125

Figure S294. Get High-res Image Gene #28: 'amp_11q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S295. Gene #29: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 29(11Q14.1) MUTATED	47	3	4	0	5
AMP PEAK 29(11Q14.1) WILD-TYPE	122	302	15	9	32

Figure S295. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S296. Gene #29: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 29(11Q14.1) MUTATED	35	7	8
AMP PEAK 29(11Q14.1) WILD-TYPE	130	82	163

Figure S296. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'RPPA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S297. Gene #29: 'amp_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 29(11Q14.1) MUTATED	5	13	31
AMP PEAK 29(11Q14.1) WILD-TYPE	120	138	126

Figure S297. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_11q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00219 (Fisher's exact test), Q value = 0.0028

Table S298. Gene #29: 'amp_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 29(11Q14.1) MUTATED	4	32	9	4
AMP PEAK 29(11Q14.1) WILD-TYPE	104	150	84	46

Figure S298. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S299. Gene #29: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 29(11Q14.1) MUTATED	44	5	9
AMP PEAK 29(11Q14.1) WILD-TYPE	190	148	141

Figure S299. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S300. Gene #29: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 29(11Q14.1) MUTATED	33	1	4	2	9	7	2
AMP PEAK 29(11Q14.1) WILD-TYPE	90	52	43	63	99	59	73

Figure S300. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00017

Table S301. Gene #29: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 29(11Q14.1) MUTATED	40	7	12
AMP PEAK 29(11Q14.1) WILD-TYPE	183	143	145

Figure S301. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S302. Gene #29: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 29(11Q14.1) MUTATED	23	1	8	27
AMP PEAK 29(11Q14.1) WILD-TYPE	196	57	129	89

Figure S302. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.02

Table S303. Gene #29: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 29(11Q14.1) MUTATED	30	9	9
AMP PEAK 29(11Q14.1) WILD-TYPE	142	87	121

Figure S303. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.029

Table S304. Gene #29: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 29(11Q14.1) MUTATED	26	9	13
AMP PEAK 29(11Q14.1) WILD-TYPE	118	106	126

Figure S304. Get High-res Image Gene #29: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S305. Gene #30: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 30(12P12.1) MUTATED	61	16	7	3	6
AMP PEAK 30(12P12.1) WILD-TYPE	108	289	12	6	31

Figure S305. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S306. Gene #30: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 30(12P12.1) MUTATED	55	12	10
AMP PEAK 30(12P12.1) WILD-TYPE	110	77	161

Figure S306. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p12.1' versus 'RPPA_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0022

Table S307. Gene #30: 'amp_12p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 30(12P12.1) MUTATED	11	27	39
AMP PEAK 30(12P12.1) WILD-TYPE	114	124	118

Figure S307. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00157 (Fisher's exact test), Q value = 0.002

Table S308. Gene #30: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 30(12P12.1) MUTATED	12	48	12	5
AMP PEAK 30(12P12.1) WILD-TYPE	96	134	81	45

Figure S308. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S309. Gene #30: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 30(12P12.1) MUTATED	70	11	12
AMP PEAK 30(12P12.1) WILD-TYPE	164	142	138

Figure S309. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S310. Gene #30: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 30(12P12.1) MUTATED	48	2	11	6	13	4	9
AMP PEAK 30(12P12.1) WILD-TYPE	75	51	36	59	95	62	66

Figure S310. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S311. Gene #30: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 30(12P12.1) MUTATED	65	16	12
AMP PEAK 30(12P12.1) WILD-TYPE	158	134	145

Figure S311. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S312. Gene #30: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 30(12P12.1) MUTATED	34	5	12	42
AMP PEAK 30(12P12.1) WILD-TYPE	185	53	125	74

Figure S312. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00068

Table S313. Gene #30: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 30(12P12.1) MUTATED	47	13	14
AMP PEAK 30(12P12.1) WILD-TYPE	125	83	116

Figure S313. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S314. Gene #30: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 30(12P12.1) MUTATED	44	10	20
AMP PEAK 30(12P12.1) WILD-TYPE	100	105	119

Figure S314. Get High-res Image Gene #30: 'amp_12p12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S315. Gene #31: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 31(12Q13.11) MUTATED	59	13	7	3	5
AMP PEAK 31(12Q13.11) WILD-TYPE	110	292	12	6	32

Figure S315. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S316. Gene #31: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 31(12Q13.11) MUTATED	49	15	7
AMP PEAK 31(12Q13.11) WILD-TYPE	116	74	164

Figure S316. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.11' versus 'RPPA_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 8e-04

Table S317. Gene #31: 'amp_12q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 31(12Q13.11) MUTATED	11	21	40
AMP PEAK 31(12Q13.11) WILD-TYPE	114	130	117

Figure S317. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q13.11' versus 'RPPA_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.00081

Table S318. Gene #31: 'amp_12q13.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 31(12Q13.11) MUTATED	9	46	12	5
AMP PEAK 31(12Q13.11) WILD-TYPE	99	136	81	45

Figure S318. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q13.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S319. Gene #31: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 31(12Q13.11) MUTATED	66	9	11
AMP PEAK 31(12Q13.11) WILD-TYPE	168	144	139

Figure S319. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S320. Gene #31: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 31(12Q13.11) MUTATED	45	1	12	6	11	4	7
AMP PEAK 31(12Q13.11) WILD-TYPE	78	52	35	59	97	62	68

Figure S320. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S321. Gene #31: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 31(12Q13.11) MUTATED	62	14	11
AMP PEAK 31(12Q13.11) WILD-TYPE	161	136	146

Figure S321. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S322. Gene #31: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 31(12Q13.11) MUTATED	30	3	11	43
AMP PEAK 31(12Q13.11) WILD-TYPE	189	55	126	73

Figure S322. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0016

Table S323. Gene #31: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 31(12Q13.11) MUTATED	41	14	11
AMP PEAK 31(12Q13.11) WILD-TYPE	131	82	119

Figure S323. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 5e-04

Table S324. Gene #31: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 31(12Q13.11) MUTATED	37	9	20
AMP PEAK 31(12Q13.11) WILD-TYPE	107	106	119

Figure S324. Get High-res Image Gene #31: 'amp_12q13.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S325. Gene #32: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 32(12Q13.2) MUTATED	68	16	6	3	7
AMP PEAK 32(12Q13.2) WILD-TYPE	101	289	13	6	30

Figure S325. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S326. Gene #32: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 32(12Q13.2) MUTATED	55	14	13
AMP PEAK 32(12Q13.2) WILD-TYPE	110	75	158

Figure S326. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q13.2' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S327. Gene #32: 'amp_12q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 32(12Q13.2) MUTATED	8	26	44
AMP PEAK 32(12Q13.2) WILD-TYPE	117	125	113

Figure S327. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00076

Table S328. Gene #32: 'amp_12q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 32(12Q13.2) MUTATED	10	49	14	5
AMP PEAK 32(12Q13.2) WILD-TYPE	98	133	79	45

Figure S328. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S329. Gene #32: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 32(12Q13.2) MUTATED	75	9	15
AMP PEAK 32(12Q13.2) WILD-TYPE	159	144	135

Figure S329. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S330. Gene #32: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 32(12Q13.2) MUTATED	46	1	16	6	15	7	8
AMP PEAK 32(12Q13.2) WILD-TYPE	77	52	31	59	93	59	67

Figure S330. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S331. Gene #32: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 32(12Q13.2) MUTATED	71	13	14
AMP PEAK 32(12Q13.2) WILD-TYPE	152	137	143

Figure S331. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S332. Gene #32: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 32(12Q13.2) MUTATED	33	3	15	47
AMP PEAK 32(12Q13.2) WILD-TYPE	186	55	122	69

Figure S332. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S333. Gene #32: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 32(12Q13.2) MUTATED	53	12	13
AMP PEAK 32(12Q13.2) WILD-TYPE	119	84	117

Figure S333. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00023

Table S334. Gene #32: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 32(12Q13.2) MUTATED	44	13	21
AMP PEAK 32(12Q13.2) WILD-TYPE	100	102	118

Figure S334. Get High-res Image Gene #32: 'amp_12q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S335. Gene #33: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 33(13Q34) MUTATED	52	3	0	1	2
AMP PEAK 33(13Q34) WILD-TYPE	117	302	19	8	35

Figure S335. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S336. Gene #33: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 33(13Q34) MUTATED	38	11	4
AMP PEAK 33(13Q34) WILD-TYPE	127	78	167

Figure S336. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S337. Gene #33: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 33(13Q34) MUTATED	4	10	31
AMP PEAK 33(13Q34) WILD-TYPE	121	141	126

Figure S337. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S338. Gene #33: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 33(13Q34) MUTATED	1	32	9	3
AMP PEAK 33(13Q34) WILD-TYPE	107	150	84	47

Figure S338. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S339. Gene #33: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 33(13Q34) MUTATED	52	3	3
AMP PEAK 33(13Q34) WILD-TYPE	182	150	147

Figure S339. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S340. Gene #33: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 33(13Q34) MUTATED	46	0	5	2	3	1	1
AMP PEAK 33(13Q34) WILD-TYPE	77	53	42	63	105	65	74

Figure S340. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S341. Gene #33: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 33(13Q34) MUTATED	52	3	3
AMP PEAK 33(13Q34) WILD-TYPE	171	147	154

Figure S341. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S342. Gene #33: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 33(13Q34) MUTATED	14	0	4	40
AMP PEAK 33(13Q34) WILD-TYPE	205	58	133	76

Figure S342. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.00082

Table S343. Gene #33: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 33(13Q34) MUTATED	33	13	6
AMP PEAK 33(13Q34) WILD-TYPE	139	83	124

Figure S343. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S344. Gene #33: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 33(13Q34) MUTATED	32	3	17
AMP PEAK 33(13Q34) WILD-TYPE	112	112	122

Figure S344. Get High-res Image Gene #33: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.013

Table S345. Gene #34: 'amp_14q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 34(14Q24.3) MUTATED	1	5	0	1	1
AMP PEAK 34(14Q24.3) WILD-TYPE	13	4	7	6	15

Figure S345. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S346. Gene #34: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 34(14Q24.3) MUTATED	52	4	2	0	6
AMP PEAK 34(14Q24.3) WILD-TYPE	117	301	17	9	31

Figure S346. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S347. Gene #34: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 34(14Q24.3) MUTATED	37	9	8
AMP PEAK 34(14Q24.3) WILD-TYPE	128	80	163

Figure S347. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q24.3' versus 'RPPA_CNMF'

P value = 0.0127 (Fisher's exact test), Q value = 0.015

Table S348. Gene #34: 'amp_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 34(14Q24.3) MUTATED	10	10	26
AMP PEAK 34(14Q24.3) WILD-TYPE	115	141	131

Figure S348. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.014

Table S349. Gene #34: 'amp_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 34(14Q24.3) MUTATED	4	28	8	6
AMP PEAK 34(14Q24.3) WILD-TYPE	104	154	85	44

Figure S349. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S350. Gene #34: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 34(14Q24.3) MUTATED	54	3	7
AMP PEAK 34(14Q24.3) WILD-TYPE	180	150	143

Figure S350. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S351. Gene #34: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 34(14Q24.3) MUTATED	40	1	8	1	9	1	4
AMP PEAK 34(14Q24.3) WILD-TYPE	83	52	39	64	99	65	71

Figure S351. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S352. Gene #34: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 34(14Q24.3) MUTATED	44	10	8
AMP PEAK 34(14Q24.3) WILD-TYPE	179	140	149

Figure S352. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S353. Gene #34: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 34(14Q24.3) MUTATED	15	1	9	37
AMP PEAK 34(14Q24.3) WILD-TYPE	204	57	128	79

Figure S353. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0455 (Fisher's exact test), Q value = 0.051

Table S354. Gene #34: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 34(14Q24.3) MUTATED	23	8	22
AMP PEAK 34(14Q24.3) WILD-TYPE	121	107	117

Figure S354. Get High-res Image Gene #34: 'amp_14q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S355. Gene #35: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 35(14Q32.33) MUTATED	67	4	2	0	6
AMP PEAK 35(14Q32.33) WILD-TYPE	102	301	17	9	31

Figure S355. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q32.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S356. Gene #35: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 35(14Q32.33) MUTATED	48	11	9
AMP PEAK 35(14Q32.33) WILD-TYPE	117	78	162

Figure S356. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S357. Gene #35: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 35(14Q32.33) MUTATED	10	13	38
AMP PEAK 35(14Q32.33) WILD-TYPE	115	138	119

Figure S357. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q32.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.00044

Table S358. Gene #35: 'amp_14q32.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 35(14Q32.33) MUTATED	4	37	15	5
AMP PEAK 35(14Q32.33) WILD-TYPE	104	145	78	45

Figure S358. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S359. Gene #35: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 35(14Q32.33) MUTATED	61	4	13
AMP PEAK 35(14Q32.33) WILD-TYPE	173	149	137

Figure S359. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S360. Gene #35: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 35(14Q32.33) MUTATED	38	1	12	3	13	7	4
AMP PEAK 35(14Q32.33) WILD-TYPE	85	52	35	62	95	59	71

Figure S360. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S361. Gene #35: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 35(14Q32.33) MUTATED	56	9	13
AMP PEAK 35(14Q32.33) WILD-TYPE	167	141	144

Figure S361. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q32.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S362. Gene #35: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 35(14Q32.33) MUTATED	23	1	11	43
AMP PEAK 35(14Q32.33) WILD-TYPE	196	57	126	73

Figure S362. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.0035

Table S363. Gene #35: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 35(14Q32.33) MUTATED	41	14	12
AMP PEAK 35(14Q32.33) WILD-TYPE	131	82	118

Figure S363. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0258 (Fisher's exact test), Q value = 0.029

Table S364. Gene #35: 'amp_14q32.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 35(14Q32.33) MUTATED	33	12	22
AMP PEAK 35(14Q32.33) WILD-TYPE	111	103	117

Figure S364. Get High-res Image Gene #35: 'amp_14q32.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S365. Gene #36: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 36(15Q26.3) MUTATED	33	2	1	0	2
AMP PEAK 36(15Q26.3) WILD-TYPE	136	303	18	9	35

Figure S365. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.01

Table S366. Gene #36: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 36(15Q26.3) MUTATED	22	6	7
AMP PEAK 36(15Q26.3) WILD-TYPE	143	83	164

Figure S366. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'RPPA_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.0048

Table S367. Gene #36: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 36(15Q26.3) MUTATED	3	6	18
AMP PEAK 36(15Q26.3) WILD-TYPE	122	145	139

Figure S367. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S368. Gene #36: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 36(15Q26.3) MUTATED	32	3	3
AMP PEAK 36(15Q26.3) WILD-TYPE	202	150	147

Figure S368. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S369. Gene #36: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 36(15Q26.3) MUTATED	20	1	6	1	8	2	0
AMP PEAK 36(15Q26.3) WILD-TYPE	103	52	41	64	100	64	75

Figure S369. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00016

Table S370. Gene #36: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 36(15Q26.3) MUTATED	28	7	3
AMP PEAK 36(15Q26.3) WILD-TYPE	195	143	154

Figure S370. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00021

Table S371. Gene #36: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 36(15Q26.3) MUTATED	15	1	3	19
AMP PEAK 36(15Q26.3) WILD-TYPE	204	57	134	97

Figure S371. Get High-res Image Gene #36: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNA_CNMF'

P value = 0.00791 (Fisher's exact test), Q value = 0.0096

Table S372. Gene #37: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 37(16P11.2) MUTATED	0	5	0	0
AMP PEAK 37(16P11.2) WILD-TYPE	14	12	12	10

Figure S372. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_16p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00502 (Fisher's exact test), Q value = 0.0062

Table S373. Gene #37: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 37(16P11.2) MUTATED	1	4	0	0	0
AMP PEAK 37(16P11.2) WILD-TYPE	13	5	7	7	16

Figure S373. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_16p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S374. Gene #37: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 37(16P11.2) MUTATED	61	1	1	0	3
AMP PEAK 37(16P11.2) WILD-TYPE	108	304	18	9	34

Figure S374. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_16p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S375. Gene #37: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 37(16P11.2) MUTATED	39	10	8
AMP PEAK 37(16P11.2) WILD-TYPE	126	79	163

Figure S375. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_16p11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S376. Gene #37: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 37(16P11.2) MUTATED	8	10	37
AMP PEAK 37(16P11.2) WILD-TYPE	117	141	120

Figure S376. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_16p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00031

Table S377. Gene #37: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 37(16P11.2) MUTATED	3	35	12	5
AMP PEAK 37(16P11.2) WILD-TYPE	105	147	81	45

Figure S377. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_16p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S378. Gene #37: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 37(16P11.2) MUTATED	58	4	4
AMP PEAK 37(16P11.2) WILD-TYPE	176	149	146

Figure S378. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_16p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S379. Gene #37: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 37(16P11.2) MUTATED	46	3	4	1	9	3	0
AMP PEAK 37(16P11.2) WILD-TYPE	77	50	43	64	99	63	75

Figure S379. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S380. Gene #37: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 37(16P11.2) MUTATED	52	6	5
AMP PEAK 37(16P11.2) WILD-TYPE	171	144	152

Figure S380. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_16p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S381. Gene #37: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 37(16P11.2) MUTATED	22	3	4	34
AMP PEAK 37(16P11.2) WILD-TYPE	197	55	133	82

Figure S381. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0038

Table S382. Gene #37: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 37(16P11.2) MUTATED	33	11	8
AMP PEAK 37(16P11.2) WILD-TYPE	139	85	122

Figure S382. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_16p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.00078

Table S383. Gene #37: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 37(16P11.2) MUTATED	29	5	18
AMP PEAK 37(16P11.2) WILD-TYPE	115	110	121

Figure S383. Get High-res Image Gene #37: 'amp_16p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S384. Gene #38: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 38(17Q11.2) MUTATED	64	4	0	1	2
AMP PEAK 38(17Q11.2) WILD-TYPE	105	301	19	8	35

Figure S384. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S385. Gene #38: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 38(17Q11.2) MUTATED	54	6	3
AMP PEAK 38(17Q11.2) WILD-TYPE	111	83	168

Figure S385. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S386. Gene #38: 'amp_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 38(17Q11.2) MUTATED	5	12	39
AMP PEAK 38(17Q11.2) WILD-TYPE	120	139	118

Figure S386. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S387. Gene #38: 'amp_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 38(17Q11.2) MUTATED	3	36	15	2
AMP PEAK 38(17Q11.2) WILD-TYPE	105	146	78	48

Figure S387. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S388. Gene #38: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 38(17Q11.2) MUTATED	64	2	4
AMP PEAK 38(17Q11.2) WILD-TYPE	170	151	146

Figure S388. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S389. Gene #38: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 38(17Q11.2) MUTATED	50	0	9	2	6	3	0
AMP PEAK 38(17Q11.2) WILD-TYPE	73	53	38	63	102	63	75

Figure S389. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S390. Gene #38: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 38(17Q11.2) MUTATED	57	9	2
AMP PEAK 38(17Q11.2) WILD-TYPE	166	141	155

Figure S390. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S391. Gene #38: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 38(17Q11.2) MUTATED	23	1	2	42
AMP PEAK 38(17Q11.2) WILD-TYPE	196	57	135	74

Figure S391. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S392. Gene #38: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 38(17Q11.2) MUTATED	41	12	5
AMP PEAK 38(17Q11.2) WILD-TYPE	131	84	125

Figure S392. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S393. Gene #38: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 38(17Q11.2) MUTATED	37	5	16
AMP PEAK 38(17Q11.2) WILD-TYPE	107	110	123

Figure S393. Get High-res Image Gene #38: 'amp_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0029

Table S394. Gene #39: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 39(17Q12) MUTATED	0	4	1	0	0
AMP PEAK 39(17Q12) WILD-TYPE	14	5	6	7	16

Figure S394. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S395. Gene #39: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 39(17Q12) MUTATED	67	5	0	1	2
AMP PEAK 39(17Q12) WILD-TYPE	102	300	19	8	35

Figure S395. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S396. Gene #39: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 39(17Q12) MUTATED	53	8	2
AMP PEAK 39(17Q12) WILD-TYPE	112	81	169

Figure S396. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S397. Gene #39: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 39(17Q12) MUTATED	5	13	42
AMP PEAK 39(17Q12) WILD-TYPE	120	138	115

Figure S397. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S398. Gene #39: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 39(17Q12) MUTATED	4	43	7	6
AMP PEAK 39(17Q12) WILD-TYPE	104	139	86	44

Figure S398. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S399. Gene #39: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 39(17Q12) MUTATED	70	2	3
AMP PEAK 39(17Q12) WILD-TYPE	164	151	147

Figure S399. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S400. Gene #39: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 39(17Q12) MUTATED	51	0	15	2	5	2	0
AMP PEAK 39(17Q12) WILD-TYPE	72	53	32	63	103	64	75

Figure S400. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S401. Gene #39: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 39(17Q12) MUTATED	63	7	3
AMP PEAK 39(17Q12) WILD-TYPE	160	143	154

Figure S401. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S402. Gene #39: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 39(17Q12) MUTATED	19	2	3	49
AMP PEAK 39(17Q12) WILD-TYPE	200	56	134	67

Figure S402. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S403. Gene #39: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 39(17Q12) MUTATED	40	13	7
AMP PEAK 39(17Q12) WILD-TYPE	132	83	123

Figure S403. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S404. Gene #39: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 39(17Q12) MUTATED	37	3	20
AMP PEAK 39(17Q12) WILD-TYPE	107	112	119

Figure S404. Get High-res Image Gene #39: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S405. Gene #40: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 40(17Q25.1) MUTATED	0	10	1	0
AMP PEAK 40(17Q25.1) WILD-TYPE	14	7	11	10

Figure S405. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S406. Gene #40: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 40(17Q25.1) MUTATED	2	8	1	0	0
AMP PEAK 40(17Q25.1) WILD-TYPE	12	1	6	7	16

Figure S406. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S407. Gene #40: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 40(17Q25.1) MUTATED	94	5	1	1	4
AMP PEAK 40(17Q25.1) WILD-TYPE	75	300	18	8	33

Figure S407. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q25.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S408. Gene #40: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 40(17Q25.1) MUTATED	64	15	6
AMP PEAK 40(17Q25.1) WILD-TYPE	101	74	165

Figure S408. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S409. Gene #40: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 40(17Q25.1) MUTATED	13	16	56
AMP PEAK 40(17Q25.1) WILD-TYPE	112	135	101

Figure S409. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q25.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S410. Gene #40: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 40(17Q25.1) MUTATED	4	56	18	7
AMP PEAK 40(17Q25.1) WILD-TYPE	104	126	75	43

Figure S410. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S411. Gene #40: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 40(17Q25.1) MUTATED	90	5	9
AMP PEAK 40(17Q25.1) WILD-TYPE	144	148	141

Figure S411. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S412. Gene #40: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 40(17Q25.1) MUTATED	72	0	13	2	9	7	1
AMP PEAK 40(17Q25.1) WILD-TYPE	51	53	34	63	99	59	74

Figure S412. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S413. Gene #40: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 40(17Q25.1) MUTATED	82	11	8
AMP PEAK 40(17Q25.1) WILD-TYPE	141	139	149

Figure S413. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S414. Gene #40: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 40(17Q25.1) MUTATED	35	2	6	58
AMP PEAK 40(17Q25.1) WILD-TYPE	184	56	131	58

Figure S414. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S415. Gene #40: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 40(17Q25.1) MUTATED	53	21	7
AMP PEAK 40(17Q25.1) WILD-TYPE	119	75	123

Figure S415. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S416. Gene #40: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 40(17Q25.1) MUTATED	42	9	30
AMP PEAK 40(17Q25.1) WILD-TYPE	102	106	109

Figure S416. Get High-res Image Gene #40: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S417. Gene #41: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 41(18P11.31) MUTATED	87	5	3	0	1
AMP PEAK 41(18P11.31) WILD-TYPE	82	300	16	9	36

Figure S417. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S418. Gene #41: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 41(18P11.31) MUTATED	62	16	7
AMP PEAK 41(18P11.31) WILD-TYPE	103	73	164

Figure S418. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S419. Gene #41: 'amp_18p11.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 41(18P11.31) MUTATED	7	19	49
AMP PEAK 41(18P11.31) WILD-TYPE	118	132	108

Figure S419. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18p11.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S420. Gene #41: 'amp_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 41(18P11.31) MUTATED	4	50	15	6
AMP PEAK 41(18P11.31) WILD-TYPE	104	132	78	44

Figure S420. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_18p11.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S421. Gene #41: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 41(18P11.31) MUTATED	85	3	8
AMP PEAK 41(18P11.31) WILD-TYPE	149	150	142

Figure S421. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S422. Gene #41: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 41(18P11.31) MUTATED	61	1	17	1	9	4	3
AMP PEAK 41(18P11.31) WILD-TYPE	62	52	30	64	99	62	72

Figure S422. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S423. Gene #41: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 41(18P11.31) MUTATED	79	9	7
AMP PEAK 41(18P11.31) WILD-TYPE	144	141	150

Figure S423. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S424. Gene #41: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 41(18P11.31) MUTATED	28	1	6	60
AMP PEAK 41(18P11.31) WILD-TYPE	191	57	131	56

Figure S424. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S425. Gene #41: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 41(18P11.31) MUTATED	52	23	7
AMP PEAK 41(18P11.31) WILD-TYPE	120	73	123

Figure S425. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S426. Gene #41: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 41(18P11.31) MUTATED	46	6	30
AMP PEAK 41(18P11.31) WILD-TYPE	98	109	109

Figure S426. Get High-res Image Gene #41: 'amp_18p11.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S427. Gene #42: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 42(18Q11.2) MUTATED	63	3	2	0	1
AMP PEAK 42(18Q11.2) WILD-TYPE	106	302	17	9	36

Figure S427. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S428. Gene #42: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 42(18Q11.2) MUTATED	47	11	3
AMP PEAK 42(18Q11.2) WILD-TYPE	118	78	168

Figure S428. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S429. Gene #42: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 42(18Q11.2) MUTATED	6	13	37
AMP PEAK 42(18Q11.2) WILD-TYPE	119	138	120

Figure S429. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S430. Gene #42: 'amp_18q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 42(18Q11.2) MUTATED	1	39	13	3
AMP PEAK 42(18Q11.2) WILD-TYPE	107	143	80	47

Figure S430. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S431. Gene #42: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 42(18Q11.2) MUTATED	63	3	3
AMP PEAK 42(18Q11.2) WILD-TYPE	171	150	147

Figure S431. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S432. Gene #42: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 42(18Q11.2) MUTATED	49	1	9	1	6	2	1
AMP PEAK 42(18Q11.2) WILD-TYPE	74	52	38	64	102	64	74

Figure S432. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S433. Gene #42: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 42(18Q11.2) MUTATED	57	9	2
AMP PEAK 42(18Q11.2) WILD-TYPE	166	141	155

Figure S433. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S434. Gene #42: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 42(18Q11.2) MUTATED	24	1	1	42
AMP PEAK 42(18Q11.2) WILD-TYPE	195	57	136	74

Figure S434. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S435. Gene #42: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 42(18Q11.2) MUTATED	43	13	1
AMP PEAK 42(18Q11.2) WILD-TYPE	129	83	129

Figure S435. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S436. Gene #42: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 42(18Q11.2) MUTATED	35	1	21
AMP PEAK 42(18Q11.2) WILD-TYPE	109	114	118

Figure S436. Get High-res Image Gene #42: 'amp_18q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNA_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.005

Table S437. Gene #43: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 43(19P13.2) MUTATED	1	7	0	0
AMP PEAK 43(19P13.2) WILD-TYPE	13	10	12	10

Figure S437. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00023

Table S438. Gene #43: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 43(19P13.2) MUTATED	2	6	0	0	0
AMP PEAK 43(19P13.2) WILD-TYPE	12	3	7	7	16

Figure S438. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S439. Gene #43: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 43(19P13.2) MUTATED	95	0	1	0	3
AMP PEAK 43(19P13.2) WILD-TYPE	74	305	18	9	34

Figure S439. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S440. Gene #43: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 43(19P13.2) MUTATED	65	15	7
AMP PEAK 43(19P13.2) WILD-TYPE	100	74	164

Figure S440. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S441. Gene #43: 'amp_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 43(19P13.2) MUTATED	8	13	53
AMP PEAK 43(19P13.2) WILD-TYPE	117	138	104

Figure S441. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S442. Gene #43: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 43(19P13.2) MUTATED	3	54	10	7
AMP PEAK 43(19P13.2) WILD-TYPE	105	128	83	43

Figure S442. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19p13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S443. Gene #43: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 43(19P13.2) MUTATED	90	2	6
AMP PEAK 43(19P13.2) WILD-TYPE	144	151	144

Figure S443. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S444. Gene #43: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 43(19P13.2) MUTATED	76	1	6	2	8	4	1
AMP PEAK 43(19P13.2) WILD-TYPE	47	52	41	63	100	62	74

Figure S444. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S445. Gene #43: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 43(19P13.2) MUTATED	82	9	6
AMP PEAK 43(19P13.2) WILD-TYPE	141	141	151

Figure S445. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S446. Gene #43: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 43(19P13.2) MUTATED	29	1	6	61
AMP PEAK 43(19P13.2) WILD-TYPE	190	57	131	55

Figure S446. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S447. Gene #43: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 43(19P13.2) MUTATED	51	22	8
AMP PEAK 43(19P13.2) WILD-TYPE	121	74	122

Figure S447. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S448. Gene #43: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 43(19P13.2) MUTATED	47	8	26
AMP PEAK 43(19P13.2) WILD-TYPE	97	107	113

Figure S448. Get High-res Image Gene #43: 'amp_19p13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 0.00511 (Fisher's exact test), Q value = 0.0063

Table S449. Gene #44: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 44(19Q12) MUTATED	1	8	1	0
AMP PEAK 44(19Q12) WILD-TYPE	13	9	11	10

Figure S449. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S450. Gene #44: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 44(19Q12) MUTATED	2	7	1	0	0
AMP PEAK 44(19Q12) WILD-TYPE	12	2	6	7	16

Figure S450. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S451. Gene #44: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 44(19Q12) MUTATED	113	2	2	0	4
AMP PEAK 44(19Q12) WILD-TYPE	56	303	17	9	33

Figure S451. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S452. Gene #44: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 44(19Q12) MUTATED	80	18	9
AMP PEAK 44(19Q12) WILD-TYPE	85	71	162

Figure S452. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S453. Gene #44: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 44(19Q12) MUTATED	7	19	66
AMP PEAK 44(19Q12) WILD-TYPE	118	132	91

Figure S453. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S454. Gene #44: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 44(19Q12) MUTATED	3	63	19	7
AMP PEAK 44(19Q12) WILD-TYPE	105	119	74	43

Figure S454. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S455. Gene #44: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 44(19Q12) MUTATED	111	3	7
AMP PEAK 44(19Q12) WILD-TYPE	123	150	143

Figure S455. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S456. Gene #44: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 44(19Q12) MUTATED	81	1	19	3	11	5	1
AMP PEAK 44(19Q12) WILD-TYPE	42	52	28	62	97	61	74

Figure S456. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S457. Gene #44: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 44(19Q12) MUTATED	99	10	8
AMP PEAK 44(19Q12) WILD-TYPE	124	140	149

Figure S457. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S458. Gene #44: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 44(19Q12) MUTATED	37	1	7	72
AMP PEAK 44(19Q12) WILD-TYPE	182	57	130	44

Figure S458. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S459. Gene #44: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 44(19Q12) MUTATED	66	27	8
AMP PEAK 44(19Q12) WILD-TYPE	106	69	122

Figure S459. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S460. Gene #44: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 44(19Q12) MUTATED	56	10	35
AMP PEAK 44(19Q12) WILD-TYPE	88	105	104

Figure S460. Get High-res Image Gene #44: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S461. Gene #45: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 45(20P13) MUTATED	87	8	12	2	8
AMP PEAK 45(20P13) WILD-TYPE	82	297	7	7	29

Figure S461. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S462. Gene #45: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 45(20P13) MUTATED	75	16	16
AMP PEAK 45(20P13) WILD-TYPE	90	73	155

Figure S462. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p13' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S463. Gene #45: 'amp_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 45(20P13) MUTATED	16	15	57
AMP PEAK 45(20P13) WILD-TYPE	109	136	100

Figure S463. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20p13' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S464. Gene #45: 'amp_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 45(20P13) MUTATED	8	54	17	9
AMP PEAK 45(20P13) WILD-TYPE	100	128	76	41

Figure S464. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S465. Gene #45: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 45(20P13) MUTATED	90	11	15
AMP PEAK 45(20P13) WILD-TYPE	144	142	135

Figure S465. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S466. Gene #45: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 45(20P13) MUTATED	64	5	16	3	12	14	2
AMP PEAK 45(20P13) WILD-TYPE	59	48	31	62	96	52	73

Figure S466. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S467. Gene #45: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 45(20P13) MUTATED	84	17	15
AMP PEAK 45(20P13) WILD-TYPE	139	133	142

Figure S467. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S468. Gene #45: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 45(20P13) MUTATED	43	5	12	56
AMP PEAK 45(20P13) WILD-TYPE	176	53	125	60

Figure S468. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 5e-04

Table S469. Gene #45: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 45(20P13) MUTATED	57	23	18
AMP PEAK 45(20P13) WILD-TYPE	115	73	112

Figure S469. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S470. Gene #45: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 45(20P13) MUTATED	56	13	29
AMP PEAK 45(20P13) WILD-TYPE	88	102	110

Figure S470. Get High-res Image Gene #45: 'amp_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNA_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.00078

Table S471. Gene #46: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 46(20Q11.21) MUTATED	2	9	0	0
AMP PEAK 46(20Q11.21) WILD-TYPE	12	8	12	10

Figure S471. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q11.21' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S472. Gene #46: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 46(20Q11.21) MUTATED	4	7	0	0	0
AMP PEAK 46(20Q11.21) WILD-TYPE	10	2	7	7	16

Figure S472. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S473. Gene #46: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 46(20Q11.21) MUTATED	120	8	13	3	8
AMP PEAK 46(20Q11.21) WILD-TYPE	49	297	6	6	29

Figure S473. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S474. Gene #46: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 46(20Q11.21) MUTATED	89	20	24
AMP PEAK 46(20Q11.21) WILD-TYPE	76	69	147

Figure S474. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S475. Gene #46: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 46(20Q11.21) MUTATED	18	24	75
AMP PEAK 46(20Q11.21) WILD-TYPE	107	127	82

Figure S475. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q11.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S476. Gene #46: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 46(20Q11.21) MUTATED	9	76	23	9
AMP PEAK 46(20Q11.21) WILD-TYPE	99	106	70	41

Figure S476. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S477. Gene #46: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 46(20Q11.21) MUTATED	119	11	21
AMP PEAK 46(20Q11.21) WILD-TYPE	115	142	129

Figure S477. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S478. Gene #46: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 46(20Q11.21) MUTATED	80	4	21	4	21	17	4
AMP PEAK 46(20Q11.21) WILD-TYPE	43	49	26	61	87	49	71

Figure S478. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S479. Gene #46: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 46(20Q11.21) MUTATED	108	19	21
AMP PEAK 46(20Q11.21) WILD-TYPE	115	131	136

Figure S479. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S480. Gene #46: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 46(20Q11.21) MUTATED	47	5	20	76
AMP PEAK 46(20Q11.21) WILD-TYPE	172	53	117	40

Figure S480. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S481. Gene #46: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 46(20Q11.21) MUTATED	76	26	23
AMP PEAK 46(20Q11.21) WILD-TYPE	96	70	107

Figure S481. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S482. Gene #46: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 46(20Q11.21) MUTATED	69	22	34
AMP PEAK 46(20Q11.21) WILD-TYPE	75	93	105

Figure S482. Get High-res Image Gene #46: 'amp_20q11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.015

Table S483. Gene #47: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 47(20Q13.12) MUTATED	1	6	0	0
AMP PEAK 47(20Q13.12) WILD-TYPE	13	11	12	10

Figure S483. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00954 (Fisher's exact test), Q value = 0.011

Table S484. Gene #47: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 47(20Q13.12) MUTATED	3	4	0	0	0
AMP PEAK 47(20Q13.12) WILD-TYPE	11	5	7	7	16

Figure S484. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S485. Gene #47: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 47(20Q13.12) MUTATED	118	10	14	3	7
AMP PEAK 47(20Q13.12) WILD-TYPE	51	295	5	6	30

Figure S485. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S486. Gene #47: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 47(20Q13.12) MUTATED	94	20	24
AMP PEAK 47(20Q13.12) WILD-TYPE	71	69	147

Figure S486. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S487. Gene #47: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 47(20Q13.12) MUTATED	19	21	73
AMP PEAK 47(20Q13.12) WILD-TYPE	106	130	84

Figure S487. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S488. Gene #47: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 47(20Q13.12) MUTATED	10	73	21	9
AMP PEAK 47(20Q13.12) WILD-TYPE	98	109	72	41

Figure S488. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S489. Gene #47: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 47(20Q13.12) MUTATED	119	12	20
AMP PEAK 47(20Q13.12) WILD-TYPE	115	141	130

Figure S489. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S490. Gene #47: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 47(20Q13.12) MUTATED	82	4	21	4	21	15	4
AMP PEAK 47(20Q13.12) WILD-TYPE	41	49	26	61	87	51	71

Figure S490. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S491. Gene #47: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 47(20Q13.12) MUTATED	110	20	21
AMP PEAK 47(20Q13.12) WILD-TYPE	113	130	136

Figure S491. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S492. Gene #47: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 47(20Q13.12) MUTATED	52	5	19	75
AMP PEAK 47(20Q13.12) WILD-TYPE	167	53	118	41

Figure S492. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S493. Gene #47: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 47(20Q13.12) MUTATED	77	28	24
AMP PEAK 47(20Q13.12) WILD-TYPE	95	68	106

Figure S493. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S494. Gene #47: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 47(20Q13.12) MUTATED	74	21	34
AMP PEAK 47(20Q13.12) WILD-TYPE	70	94	105

Figure S494. Get High-res Image Gene #47: 'amp_20q13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNA_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.01

Table S495. Gene #48: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
AMP PEAK 48(20Q13.33) MUTATED	2	7	0	0
AMP PEAK 48(20Q13.33) WILD-TYPE	12	10	12	10

Figure S495. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0017

Table S496. Gene #48: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 48(20Q13.33) MUTATED	4	5	0	0	0
AMP PEAK 48(20Q13.33) WILD-TYPE	10	4	7	7	16

Figure S496. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S497. Gene #48: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 48(20Q13.33) MUTATED	117	11	15	3	7
AMP PEAK 48(20Q13.33) WILD-TYPE	52	294	4	6	30

Figure S497. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S498. Gene #48: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 48(20Q13.33) MUTATED	91	21	24
AMP PEAK 48(20Q13.33) WILD-TYPE	74	68	147

Figure S498. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S499. Gene #48: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 48(20Q13.33) MUTATED	20	24	72
AMP PEAK 48(20Q13.33) WILD-TYPE	105	127	85

Figure S499. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S500. Gene #48: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 48(20Q13.33) MUTATED	11	78	19	8
AMP PEAK 48(20Q13.33) WILD-TYPE	97	104	74	42

Figure S500. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S501. Gene #48: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 48(20Q13.33) MUTATED	118	14	21
AMP PEAK 48(20Q13.33) WILD-TYPE	116	139	129

Figure S501. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S502. Gene #48: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 48(20Q13.33) MUTATED	78	4	24	5	22	16	4
AMP PEAK 48(20Q13.33) WILD-TYPE	45	49	23	60	86	50	71

Figure S502. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S503. Gene #48: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 48(20Q13.33) MUTATED	109	19	22
AMP PEAK 48(20Q13.33) WILD-TYPE	114	131	135

Figure S503. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S504. Gene #48: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 48(20Q13.33) MUTATED	53	6	19	72
AMP PEAK 48(20Q13.33) WILD-TYPE	166	52	118	44

Figure S504. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S505. Gene #48: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 48(20Q13.33) MUTATED	76	28	23
AMP PEAK 48(20Q13.33) WILD-TYPE	96	68	107

Figure S505. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S506. Gene #48: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 48(20Q13.33) MUTATED	71	21	35
AMP PEAK 48(20Q13.33) WILD-TYPE	73	94	104

Figure S506. Get High-res Image Gene #48: 'amp_20q13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_22q12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S507. Gene #49: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 49(22Q12.2) MUTATED	56	4	1	1	0
AMP PEAK 49(22Q12.2) WILD-TYPE	113	301	18	8	37

Figure S507. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q12.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S508. Gene #49: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 49(22Q12.2) MUTATED	49	8	0
AMP PEAK 49(22Q12.2) WILD-TYPE	116	81	171

Figure S508. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q12.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S509. Gene #49: 'amp_22q12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 49(22Q12.2) MUTATED	5	9	38
AMP PEAK 49(22Q12.2) WILD-TYPE	120	142	119

Figure S509. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_22q12.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S510. Gene #49: 'amp_22q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 49(22Q12.2) MUTATED	1	41	6	4
AMP PEAK 49(22Q12.2) WILD-TYPE	107	141	87	46

Figure S510. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_22q12.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S511. Gene #49: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 49(22Q12.2) MUTATED	60	1	0
AMP PEAK 49(22Q12.2) WILD-TYPE	174	152	150

Figure S511. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S512. Gene #49: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 49(22Q12.2) MUTATED	43	1	15	0	2	0	0
AMP PEAK 49(22Q12.2) WILD-TYPE	80	52	32	65	106	66	75

Figure S512. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S513. Gene #49: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 49(22Q12.2) MUTATED	59	2	0
AMP PEAK 49(22Q12.2) WILD-TYPE	164	148	157

Figure S513. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_22q12.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S514. Gene #49: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 49(22Q12.2) MUTATED	16	1	0	44
AMP PEAK 49(22Q12.2) WILD-TYPE	203	57	137	72

Figure S514. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S515. Gene #49: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 49(22Q12.2) MUTATED	43	10	3
AMP PEAK 49(22Q12.2) WILD-TYPE	129	86	127

Figure S515. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q12.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S516. Gene #49: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 49(22Q12.2) MUTATED	40	1	15
AMP PEAK 49(22Q12.2) WILD-TYPE	104	114	124

Figure S516. Get High-res Image Gene #49: 'amp_22q12.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xp11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S517. Gene #50: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 50(XP11.23) MUTATED	48	8	8	3	23
AMP PEAK 50(XP11.23) WILD-TYPE	121	297	11	6	14

Figure S517. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xp11.23' versus 'METHLYATION_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00028

Table S518. Gene #50: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 50(XP11.23) MUTATED	43	11	17
AMP PEAK 50(XP11.23) WILD-TYPE	122	78	154

Figure S518. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xp11.23' versus 'RPPA_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.004

Table S519. Gene #50: 'amp_xp11.23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 50(XP11.23) MUTATED	16	16	38
AMP PEAK 50(XP11.23) WILD-TYPE	109	135	119

Figure S519. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00027

Table S520. Gene #50: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 50(XP11.23) MUTATED	57	15	18
AMP PEAK 50(XP11.23) WILD-TYPE	177	138	132

Figure S520. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xp11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00044 (Fisher's exact test), Q value = 6e-04

Table S521. Gene #50: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 50(XP11.23) MUTATED	38	5	10	6	14	9	8
AMP PEAK 50(XP11.23) WILD-TYPE	85	48	37	59	94	57	67

Figure S521. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00031

Table S522. Gene #50: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 50(XP11.23) MUTATED	55	18	16
AMP PEAK 50(XP11.23) WILD-TYPE	168	132	141

Figure S522. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xp11.23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0031

Table S523. Gene #50: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 50(XP11.23) MUTATED	34	6	16	33
AMP PEAK 50(XP11.23) WILD-TYPE	185	52	121	83

Figure S523. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xp11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00915 (Fisher's exact test), Q value = 0.011

Table S524. Gene #50: 'amp_xp11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 50(XP11.23) MUTATED	40	15	13
AMP PEAK 50(XP11.23) WILD-TYPE	132	81	117

Figure S524. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_xp11.23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00998 (Fisher's exact test), Q value = 0.012

Table S525. Gene #50: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
AMP PEAK 50(XP11.23) MUTATED	32	10	26
AMP PEAK 50(XP11.23) WILD-TYPE	112	105	113

Figure S525. Get High-res Image Gene #50: 'amp_xp11.23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_xq28' versus 'MRNA_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.031

Table S526. Gene #51: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
AMP PEAK 51(XQ28) MUTATED	1	5	1	1	1
AMP PEAK 51(XQ28) WILD-TYPE	13	4	6	6	15

Figure S526. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S527. Gene #51: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
AMP PEAK 51(XQ28) MUTATED	49	10	8	3	23
AMP PEAK 51(XQ28) WILD-TYPE	120	295	11	6	14

Figure S527. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.035

Table S528. Gene #51: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
AMP PEAK 51(XQ28) MUTATED	37	14	20
AMP PEAK 51(XQ28) WILD-TYPE	128	75	151

Figure S528. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S529. Gene #51: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
AMP PEAK 51(XQ28) MUTATED	16	18	46
AMP PEAK 51(XQ28) WILD-TYPE	109	133	111

Figure S529. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_xq28' versus 'RPPA_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.042

Table S530. Gene #51: 'amp_xq28' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
AMP PEAK 51(XQ28) MUTATED	16	45	14	5
AMP PEAK 51(XQ28) WILD-TYPE	92	137	79	45

Figure S530. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0012

Table S531. Gene #51: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
AMP PEAK 51(XQ28) MUTATED	57	17	19
AMP PEAK 51(XQ28) WILD-TYPE	177	136	131

Figure S531. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00238 (Fisher's exact test), Q value = 0.003

Table S532. Gene #51: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
AMP PEAK 51(XQ28) MUTATED	37	6	10	6	17	9	8
AMP PEAK 51(XQ28) WILD-TYPE	86	47	37	59	91	57	67

Figure S532. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.0031

Table S533. Gene #51: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
AMP PEAK 51(XQ28) MUTATED	52	22	16
AMP PEAK 51(XQ28) WILD-TYPE	171	128	141

Figure S533. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.015

Table S534. Gene #51: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
AMP PEAK 51(XQ28) MUTATED	36	7	16	31
AMP PEAK 51(XQ28) WILD-TYPE	183	51	121	85

Figure S534. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.02

Table S535. Gene #51: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
AMP PEAK 51(XQ28) MUTATED	40	16	14
AMP PEAK 51(XQ28) WILD-TYPE	132	80	116

Figure S535. Get High-res Image Gene #51: 'amp_xq28' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MRNA_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.028

Table S536. Gene #52: 'del_1p36.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 1(1P36.21) MUTATED	2	6	0	0
DEL PEAK 1(1P36.21) WILD-TYPE	12	11	12	10

Figure S536. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.0023

Table S537. Gene #52: 'del_1p36.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 1(1P36.21) MUTATED	3	5	0	0	0
DEL PEAK 1(1P36.21) WILD-TYPE	11	4	7	7	16

Figure S537. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S538. Gene #52: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 1(1P36.21) MUTATED	60	3	3	5	0
DEL PEAK 1(1P36.21) WILD-TYPE	109	302	16	4	37

Figure S538. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S539. Gene #52: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 1(1P36.21) MUTATED	39	15	6
DEL PEAK 1(1P36.21) WILD-TYPE	126	74	165

Figure S539. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.21' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00035

Table S540. Gene #52: 'del_1p36.21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 1(1P36.21) MUTATED	6	15	32
DEL PEAK 1(1P36.21) WILD-TYPE	119	136	125

Figure S540. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S541. Gene #52: 'del_1p36.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 1(1P36.21) MUTATED	1	35	9	8
DEL PEAK 1(1P36.21) WILD-TYPE	107	147	84	42

Figure S541. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S542. Gene #52: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 1(1P36.21) MUTATED	61	6	4
DEL PEAK 1(1P36.21) WILD-TYPE	173	147	146

Figure S542. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S543. Gene #52: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 1(1P36.21) MUTATED	42	1	9	4	12	3	0
DEL PEAK 1(1P36.21) WILD-TYPE	81	52	38	61	96	63	75

Figure S543. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S544. Gene #52: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 1(1P36.21) MUTATED	53	9	6
DEL PEAK 1(1P36.21) WILD-TYPE	170	141	151

Figure S544. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S545. Gene #52: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 1(1P36.21) MUTATED	27	0	3	38
DEL PEAK 1(1P36.21) WILD-TYPE	192	58	134	78

Figure S545. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00147 (Fisher's exact test), Q value = 0.0019

Table S546. Gene #52: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 1(1P36.21) MUTATED	24	25	11
DEL PEAK 1(1P36.21) WILD-TYPE	148	71	119

Figure S546. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00035

Table S547. Gene #52: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 1(1P36.21) MUTATED	27	5	28
DEL PEAK 1(1P36.21) WILD-TYPE	117	110	111

Figure S547. Get High-res Image Gene #52: 'del_1p36.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0077 (Fisher's exact test), Q value = 0.0093

Table S548. Gene #53: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 2(1P36.11) MUTATED	2	4	0	0	0
DEL PEAK 2(1P36.11) WILD-TYPE	12	5	7	7	16

Figure S548. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S549. Gene #53: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 2(1P36.11) MUTATED	72	2	4	5	0
DEL PEAK 2(1P36.11) WILD-TYPE	97	303	15	4	37

Figure S549. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S550. Gene #53: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 2(1P36.11) MUTATED	56	12	6
DEL PEAK 2(1P36.11) WILD-TYPE	109	77	165

Figure S550. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S551. Gene #53: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 2(1P36.11) MUTATED	7	18	40
DEL PEAK 2(1P36.11) WILD-TYPE	118	133	117

Figure S551. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S552. Gene #53: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 2(1P36.11) MUTATED	2	43	13	7
DEL PEAK 2(1P36.11) WILD-TYPE	106	139	80	43

Figure S552. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_1p36.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S553. Gene #53: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 2(1P36.11) MUTATED	73	6	4
DEL PEAK 2(1P36.11) WILD-TYPE	161	147	146

Figure S553. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S554. Gene #53: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 2(1P36.11) MUTATED	51	1	10	4	14	3	0
DEL PEAK 2(1P36.11) WILD-TYPE	72	52	37	61	94	63	75

Figure S554. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S555. Gene #53: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 2(1P36.11) MUTATED	64	9	7
DEL PEAK 2(1P36.11) WILD-TYPE	159	141	150

Figure S555. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S556. Gene #53: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 2(1P36.11) MUTATED	33	0	3	44
DEL PEAK 2(1P36.11) WILD-TYPE	186	58	134	72

Figure S556. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0013

Table S557. Gene #53: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 2(1P36.11) MUTATED	40	22	11
DEL PEAK 2(1P36.11) WILD-TYPE	132	74	119

Figure S557. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S558. Gene #53: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 2(1P36.11) MUTATED	42	6	25
DEL PEAK 2(1P36.11) WILD-TYPE	102	109	114

Figure S558. Get High-res Image Gene #53: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S559. Gene #54: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 3(2P25.3) MUTATED	24	2	0	0	0
DEL PEAK 3(2P25.3) WILD-TYPE	145	303	19	9	37

Figure S559. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'METHLYATION_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00021

Table S560. Gene #54: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 3(2P25.3) MUTATED	19	4	2
DEL PEAK 3(2P25.3) WILD-TYPE	146	85	169

Figure S560. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2p25.3' versus 'RPPA_CNMF'

P value = 0.00395 (Fisher's exact test), Q value = 0.0049

Table S561. Gene #54: 'del_2p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 3(2P25.3) MUTATED	2	3	14
DEL PEAK 3(2P25.3) WILD-TYPE	123	148	143

Figure S561. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2p25.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S562. Gene #54: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 3(2P25.3) MUTATED	22	1	3
DEL PEAK 3(2P25.3) WILD-TYPE	212	152	147

Figure S562. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00032

Table S563. Gene #54: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 3(2P25.3) MUTATED	16	1	3	0	3	3	0
DEL PEAK 3(2P25.3) WILD-TYPE	107	52	44	65	105	63	75

Figure S563. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.0016

Table S564. Gene #54: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 3(2P25.3) MUTATED	20	3	3
DEL PEAK 3(2P25.3) WILD-TYPE	203	147	154

Figure S564. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.00099

Table S565. Gene #54: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 3(2P25.3) MUTATED	7	1	3	15
DEL PEAK 3(2P25.3) WILD-TYPE	212	57	134	101

Figure S565. Get High-res Image Gene #54: 'del_2p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MRNA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.044

Table S566. Gene #55: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 4(2Q22.1) MUTATED	0	4	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	14	13	12	10

Figure S566. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 9e-04

Table S567. Gene #55: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 4(2Q22.1) MUTATED	0	4	0	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	14	5	7	7	16

Figure S567. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S568. Gene #55: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 4(2Q22.1) MUTATED	46	0	2	0	0
DEL PEAK 4(2Q22.1) WILD-TYPE	123	305	17	9	37

Figure S568. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S569. Gene #55: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 4(2Q22.1) MUTATED	30	8	4
DEL PEAK 4(2Q22.1) WILD-TYPE	135	81	167

Figure S569. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S570. Gene #55: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 4(2Q22.1) MUTATED	2	8	29
DEL PEAK 4(2Q22.1) WILD-TYPE	123	143	128

Figure S570. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00103 (Fisher's exact test), Q value = 0.0014

Table S571. Gene #55: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 4(2Q22.1) MUTATED	1	22	12	4
DEL PEAK 4(2Q22.1) WILD-TYPE	107	160	81	46

Figure S571. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S572. Gene #55: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 4(2Q22.1) MUTATED	43	0	5
DEL PEAK 4(2Q22.1) WILD-TYPE	191	153	145

Figure S572. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S573. Gene #55: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 4(2Q22.1) MUTATED	31	0	3	0	9	5	0
DEL PEAK 4(2Q22.1) WILD-TYPE	92	53	44	65	99	61	75

Figure S573. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S574. Gene #55: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 4(2Q22.1) MUTATED	37	5	4
DEL PEAK 4(2Q22.1) WILD-TYPE	186	145	153

Figure S574. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S575. Gene #55: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 4(2Q22.1) MUTATED	19	0	4	23
DEL PEAK 4(2Q22.1) WILD-TYPE	200	58	133	93

Figure S575. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0012

Table S576. Gene #55: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 4(2Q22.1) MUTATED	29	5	7
DEL PEAK 4(2Q22.1) WILD-TYPE	143	91	123

Figure S576. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00104 (Fisher's exact test), Q value = 0.0014

Table S577. Gene #55: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 4(2Q22.1) MUTATED	26	7	8
DEL PEAK 4(2Q22.1) WILD-TYPE	118	108	131

Figure S577. Get High-res Image Gene #55: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S578. Gene #56: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 5(2Q37.3) MUTATED	49	1	2	0	1
DEL PEAK 5(2Q37.3) WILD-TYPE	120	304	17	9	36

Figure S578. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S579. Gene #56: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 5(2Q37.3) MUTATED	35	6	8
DEL PEAK 5(2Q37.3) WILD-TYPE	130	83	163

Figure S579. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S580. Gene #56: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 5(2Q37.3) MUTATED	5	5	28
DEL PEAK 5(2Q37.3) WILD-TYPE	120	146	129

Figure S580. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00479 (Fisher's exact test), Q value = 0.0059

Table S581. Gene #56: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 5(2Q37.3) MUTATED	2	24	7	5
DEL PEAK 5(2Q37.3) WILD-TYPE	106	158	86	45

Figure S581. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S582. Gene #56: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 5(2Q37.3) MUTATED	42	3	7
DEL PEAK 5(2Q37.3) WILD-TYPE	192	150	143

Figure S582. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S583. Gene #56: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 5(2Q37.3) MUTATED	24	0	9	3	10	6	0
DEL PEAK 5(2Q37.3) WILD-TYPE	99	53	38	62	98	60	75

Figure S583. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S584. Gene #56: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 5(2Q37.3) MUTATED	39	5	8
DEL PEAK 5(2Q37.3) WILD-TYPE	184	145	149

Figure S584. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.001

Table S585. Gene #56: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 5(2Q37.3) MUTATED	21	1	8	22
DEL PEAK 5(2Q37.3) WILD-TYPE	198	57	129	94

Figure S585. Get High-res Image Gene #56: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00791 (Fisher's exact test), Q value = 0.0096

Table S586. Gene #57: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 6(3P14.2) MUTATED	2	4	0	0	0
DEL PEAK 6(3P14.2) WILD-TYPE	12	5	7	7	16

Figure S586. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S587. Gene #57: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 6(3P14.2) MUTATED	72	0	4	2	1
DEL PEAK 6(3P14.2) WILD-TYPE	97	305	15	7	36

Figure S587. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S588. Gene #57: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 6(3P14.2) MUTATED	51	12	5
DEL PEAK 6(3P14.2) WILD-TYPE	114	77	166

Figure S588. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p14.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S589. Gene #57: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 6(3P14.2) MUTATED	6	15	42
DEL PEAK 6(3P14.2) WILD-TYPE	119	136	115

Figure S589. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p14.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S590. Gene #57: 'del_3p14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 6(3P14.2) MUTATED	2	47	12	2
DEL PEAK 6(3P14.2) WILD-TYPE	106	135	81	48

Figure S590. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S591. Gene #57: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 6(3P14.2) MUTATED	73	1	4
DEL PEAK 6(3P14.2) WILD-TYPE	161	152	146

Figure S591. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S592. Gene #57: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 6(3P14.2) MUTATED	49	0	12	0	12	5	0
DEL PEAK 6(3P14.2) WILD-TYPE	74	53	35	65	96	61	75

Figure S592. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S593. Gene #57: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 6(3P14.2) MUTATED	62	11	4
DEL PEAK 6(3P14.2) WILD-TYPE	161	139	153

Figure S593. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S594. Gene #57: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 6(3P14.2) MUTATED	34	1	3	39
DEL PEAK 6(3P14.2) WILD-TYPE	185	57	134	77

Figure S594. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00052

Table S595. Gene #57: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 6(3P14.2) MUTATED	41	16	9
DEL PEAK 6(3P14.2) WILD-TYPE	131	80	121

Figure S595. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S596. Gene #57: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 6(3P14.2) MUTATED	42	4	20
DEL PEAK 6(3P14.2) WILD-TYPE	102	111	119

Figure S596. Get High-res Image Gene #57: 'del_3p14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3q13.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S597. Gene #58: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 7(3Q13.31) MUTATED	36	4	0	2	1
DEL PEAK 7(3Q13.31) WILD-TYPE	133	301	19	7	36

Figure S597. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3q13.31' versus 'METHLYATION_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.00069

Table S598. Gene #58: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 7(3Q13.31) MUTATED	24	7	5
DEL PEAK 7(3Q13.31) WILD-TYPE	141	82	166

Figure S598. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3q13.31' versus 'RPPA_CNMF'

P value = 0.00455 (Fisher's exact test), Q value = 0.0056

Table S599. Gene #58: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 7(3Q13.31) MUTATED	3	11	20
DEL PEAK 7(3Q13.31) WILD-TYPE	122	140	137

Figure S599. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3q13.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.00407 (Fisher's exact test), Q value = 0.005

Table S600. Gene #58: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 7(3Q13.31) MUTATED	1	21	8	4
DEL PEAK 7(3Q13.31) WILD-TYPE	107	161	85	46

Figure S600. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3q13.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S601. Gene #58: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 7(3Q13.31) MUTATED	35	2	6
DEL PEAK 7(3Q13.31) WILD-TYPE	199	151	144

Figure S601. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3q13.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S602. Gene #58: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 7(3Q13.31) MUTATED	28	2	4	0	3	5	1
DEL PEAK 7(3Q13.31) WILD-TYPE	95	51	43	65	105	61	74

Figure S602. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S603. Gene #58: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 7(3Q13.31) MUTATED	32	4	5
DEL PEAK 7(3Q13.31) WILD-TYPE	191	146	152

Figure S603. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3q13.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S604. Gene #58: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 7(3Q13.31) MUTATED	13	2	4	22
DEL PEAK 7(3Q13.31) WILD-TYPE	206	56	133	94

Figure S604. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3q13.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.018

Table S605. Gene #58: 'del_3q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 7(3Q13.31) MUTATED	19	11	4
DEL PEAK 7(3Q13.31) WILD-TYPE	153	85	126

Figure S605. Get High-res Image Gene #58: 'del_3q13.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.015

Table S606. Gene #59: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 8(4P16.3) MUTATED	1	6	0	0
DEL PEAK 8(4P16.3) WILD-TYPE	13	11	12	10

Figure S606. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00136 (Fisher's exact test), Q value = 0.0018

Table S607. Gene #59: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 8(4P16.3) MUTATED	2	5	0	0	0
DEL PEAK 8(4P16.3) WILD-TYPE	12	4	7	7	16

Figure S607. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S608. Gene #59: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 8(4P16.3) MUTATED	79	4	5	4	2
DEL PEAK 8(4P16.3) WILD-TYPE	90	301	14	5	35

Figure S608. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S609. Gene #59: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 8(4P16.3) MUTATED	62	13	7
DEL PEAK 8(4P16.3) WILD-TYPE	103	76	164

Figure S609. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S610. Gene #59: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 8(4P16.3) MUTATED	10	21	44
DEL PEAK 8(4P16.3) WILD-TYPE	115	130	113

Figure S610. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S611. Gene #59: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 8(4P16.3) MUTATED	5	46	15	9
DEL PEAK 8(4P16.3) WILD-TYPE	103	136	78	41

Figure S611. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S612. Gene #59: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 8(4P16.3) MUTATED	79	6	9
DEL PEAK 8(4P16.3) WILD-TYPE	155	147	141

Figure S612. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S613. Gene #59: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 8(4P16.3) MUTATED	55	1	15	2	14	6	1
DEL PEAK 8(4P16.3) WILD-TYPE	68	52	32	63	94	60	74

Figure S613. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S614. Gene #59: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 8(4P16.3) MUTATED	70	12	9
DEL PEAK 8(4P16.3) WILD-TYPE	153	138	148

Figure S614. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S615. Gene #59: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 8(4P16.3) MUTATED	32	1	6	52
DEL PEAK 8(4P16.3) WILD-TYPE	187	57	131	64

Figure S615. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S616. Gene #59: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 8(4P16.3) MUTATED	46	24	10
DEL PEAK 8(4P16.3) WILD-TYPE	126	72	120

Figure S616. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S617. Gene #59: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 8(4P16.3) MUTATED	45	8	27
DEL PEAK 8(4P16.3) WILD-TYPE	99	107	112

Figure S617. Get High-res Image Gene #59: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.015

Table S618. Gene #60: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 9(4P15.2) MUTATED	1	6	0	0
DEL PEAK 9(4P15.2) WILD-TYPE	13	11	12	10

Figure S618. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0097 (Fisher's exact test), Q value = 0.012

Table S619. Gene #60: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 9(4P15.2) MUTATED	3	4	0	0	0
DEL PEAK 9(4P15.2) WILD-TYPE	11	5	7	7	16

Figure S619. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p15.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S620. Gene #60: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 9(4P15.2) MUTATED	84	3	5	4	2
DEL PEAK 9(4P15.2) WILD-TYPE	85	302	14	5	35

Figure S620. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S621. Gene #60: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 9(4P15.2) MUTATED	67	14	6
DEL PEAK 9(4P15.2) WILD-TYPE	98	75	165

Figure S621. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S622. Gene #60: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 9(4P15.2) MUTATED	8	22	49
DEL PEAK 9(4P15.2) WILD-TYPE	117	129	108

Figure S622. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p15.2' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S623. Gene #60: 'del_4p15.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 9(4P15.2) MUTATED	5	51	15	8
DEL PEAK 9(4P15.2) WILD-TYPE	103	131	78	42

Figure S623. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S624. Gene #60: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 9(4P15.2) MUTATED	84	6	8
DEL PEAK 9(4P15.2) WILD-TYPE	150	147	142

Figure S624. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p15.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S625. Gene #60: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 9(4P15.2) MUTATED	57	1	15	2	17	5	1
DEL PEAK 9(4P15.2) WILD-TYPE	66	52	32	63	91	61	74

Figure S625. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S626. Gene #60: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 9(4P15.2) MUTATED	76	12	8
DEL PEAK 9(4P15.2) WILD-TYPE	147	138	149

Figure S626. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S627. Gene #60: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 9(4P15.2) MUTATED	36	1	5	54
DEL PEAK 9(4P15.2) WILD-TYPE	183	57	132	62

Figure S627. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S628. Gene #60: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 9(4P15.2) MUTATED	52	24	10
DEL PEAK 9(4P15.2) WILD-TYPE	120	72	120

Figure S628. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S629. Gene #60: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 9(4P15.2) MUTATED	49	7	30
DEL PEAK 9(4P15.2) WILD-TYPE	95	108	109

Figure S629. Get High-res Image Gene #60: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.0049

Table S630. Gene #61: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 10(4Q22.1) MUTATED	1	7	0	0
DEL PEAK 10(4Q22.1) WILD-TYPE	13	10	12	10

Figure S630. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 2e-04

Table S631. Gene #61: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 10(4Q22.1) MUTATED	2	6	0	0	0
DEL PEAK 10(4Q22.1) WILD-TYPE	12	3	7	7	16

Figure S631. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S632. Gene #61: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 10(4Q22.1) MUTATED	94	2	4	4	2
DEL PEAK 10(4Q22.1) WILD-TYPE	75	303	15	5	35

Figure S632. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S633. Gene #61: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 10(4Q22.1) MUTATED	71	16	5
DEL PEAK 10(4Q22.1) WILD-TYPE	94	73	166

Figure S633. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S634. Gene #61: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 10(4Q22.1) MUTATED	11	18	55
DEL PEAK 10(4Q22.1) WILD-TYPE	114	133	102

Figure S634. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q22.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S635. Gene #61: 'del_4q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 10(4Q22.1) MUTATED	4	53	18	9
DEL PEAK 10(4Q22.1) WILD-TYPE	104	129	75	41

Figure S635. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S636. Gene #61: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 10(4Q22.1) MUTATED	94	5	7
DEL PEAK 10(4Q22.1) WILD-TYPE	140	148	143

Figure S636. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S637. Gene #61: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 10(4Q22.1) MUTATED	68	1	12	2	18	5	0
DEL PEAK 10(4Q22.1) WILD-TYPE	55	52	35	63	90	61	75

Figure S637. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S638. Gene #61: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 10(4Q22.1) MUTATED	86	10	7
DEL PEAK 10(4Q22.1) WILD-TYPE	137	140	150

Figure S638. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S639. Gene #61: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 10(4Q22.1) MUTATED	38	0	3	62
DEL PEAK 10(4Q22.1) WILD-TYPE	181	58	134	54

Figure S639. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S640. Gene #61: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 10(4Q22.1) MUTATED	56	26	8
DEL PEAK 10(4Q22.1) WILD-TYPE	116	70	122

Figure S640. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S641. Gene #61: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 10(4Q22.1) MUTATED	48	5	37
DEL PEAK 10(4Q22.1) WILD-TYPE	96	110	102

Figure S641. Get High-res Image Gene #61: 'del_4q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q34.3' versus 'MRNA_CNMF'

P value = 0.00398 (Fisher's exact test), Q value = 0.0049

Table S642. Gene #62: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 11(4Q34.3) MUTATED	1	7	0	0
DEL PEAK 11(4Q34.3) WILD-TYPE	13	10	12	10

Figure S642. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q34.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00021

Table S643. Gene #62: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 11(4Q34.3) MUTATED	2	6	0	0	0
DEL PEAK 11(4Q34.3) WILD-TYPE	12	3	7	7	16

Figure S643. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q34.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S644. Gene #62: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 11(4Q34.3) MUTATED	111	6	6	4	3
DEL PEAK 11(4Q34.3) WILD-TYPE	58	299	13	5	34

Figure S644. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q34.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S645. Gene #62: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 11(4Q34.3) MUTATED	81	22	11
DEL PEAK 11(4Q34.3) WILD-TYPE	84	67	160

Figure S645. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q34.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S646. Gene #62: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 11(4Q34.3) MUTATED	16	22	66
DEL PEAK 11(4Q34.3) WILD-TYPE	109	129	91

Figure S646. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q34.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S647. Gene #62: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 11(4Q34.3) MUTATED	7	66	22	9
DEL PEAK 11(4Q34.3) WILD-TYPE	101	116	71	41

Figure S647. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q34.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S648. Gene #62: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 11(4Q34.3) MUTATED	114	8	8
DEL PEAK 11(4Q34.3) WILD-TYPE	120	145	142

Figure S648. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q34.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S649. Gene #62: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 11(4Q34.3) MUTATED	81	1	16	3	23	6	0
DEL PEAK 11(4Q34.3) WILD-TYPE	42	52	31	62	85	60	75

Figure S649. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S650. Gene #62: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 11(4Q34.3) MUTATED	99	20	8
DEL PEAK 11(4Q34.3) WILD-TYPE	124	130	149

Figure S650. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q34.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S651. Gene #62: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 11(4Q34.3) MUTATED	51	1	5	70
DEL PEAK 11(4Q34.3) WILD-TYPE	168	57	132	46

Figure S651. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q34.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S652. Gene #62: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 11(4Q34.3) MUTATED	66	33	13
DEL PEAK 11(4Q34.3) WILD-TYPE	106	63	117

Figure S652. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q34.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S653. Gene #62: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 11(4Q34.3) MUTATED	59	7	46
DEL PEAK 11(4Q34.3) WILD-TYPE	85	108	93

Figure S653. Get High-res Image Gene #62: 'del_4q34.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.015

Table S654. Gene #63: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 12(5Q12.1) MUTATED	1	6	0	0
DEL PEAK 12(5Q12.1) WILD-TYPE	13	11	12	10

Figure S654. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q12.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00925 (Fisher's exact test), Q value = 0.011

Table S655. Gene #63: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 12(5Q12.1) MUTATED	3	4	0	0	0
DEL PEAK 12(5Q12.1) WILD-TYPE	11	5	7	7	16

Figure S655. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S656. Gene #63: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 12(5Q12.1) MUTATED	103	0	2	2	4
DEL PEAK 12(5Q12.1) WILD-TYPE	66	305	17	7	33

Figure S656. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q12.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S657. Gene #63: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 12(5Q12.1) MUTATED	75	14	8
DEL PEAK 12(5Q12.1) WILD-TYPE	90	75	163

Figure S657. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S658. Gene #63: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 12(5Q12.1) MUTATED	8	24	54
DEL PEAK 12(5Q12.1) WILD-TYPE	117	127	103

Figure S658. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q12.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S659. Gene #63: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 12(5Q12.1) MUTATED	0	58	19	9
DEL PEAK 12(5Q12.1) WILD-TYPE	108	124	74	41

Figure S659. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S660. Gene #63: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 12(5Q12.1) MUTATED	96	4	10
DEL PEAK 12(5Q12.1) WILD-TYPE	138	149	140

Figure S660. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S661. Gene #63: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 12(5Q12.1) MUTATED	69	0	11	2	18	10	0
DEL PEAK 12(5Q12.1) WILD-TYPE	54	53	36	63	90	56	75

Figure S661. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S662. Gene #63: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 12(5Q12.1) MUTATED	88	12	10
DEL PEAK 12(5Q12.1) WILD-TYPE	135	138	147

Figure S662. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S663. Gene #63: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 12(5Q12.1) MUTATED	44	0	8	58
DEL PEAK 12(5Q12.1) WILD-TYPE	175	58	129	58

Figure S663. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S664. Gene #63: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 12(5Q12.1) MUTATED	61	22	12
DEL PEAK 12(5Q12.1) WILD-TYPE	111	74	118

Figure S664. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q12.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S665. Gene #63: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 12(5Q12.1) MUTATED	54	10	31
DEL PEAK 12(5Q12.1) WILD-TYPE	90	105	108

Figure S665. Get High-res Image Gene #63: 'del_5q12.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.033

Table S666. Gene #64: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 13(6Q26) MUTATED	1	3	0	0	0
DEL PEAK 13(6Q26) WILD-TYPE	13	6	7	7	16

Figure S666. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S667. Gene #64: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 13(6Q26) MUTATED	39	4	2	1	0
DEL PEAK 13(6Q26) WILD-TYPE	130	301	17	8	37

Figure S667. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S668. Gene #64: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 13(6Q26) MUTATED	31	8	1
DEL PEAK 13(6Q26) WILD-TYPE	134	81	170

Figure S668. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'RPPA_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.0016

Table S669. Gene #64: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 13(6Q26) MUTATED	1	23	7	5
DEL PEAK 13(6Q26) WILD-TYPE	107	159	86	45

Figure S669. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S670. Gene #64: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 13(6Q26) MUTATED	42	2	2
DEL PEAK 13(6Q26) WILD-TYPE	192	151	148

Figure S670. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S671. Gene #64: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 13(6Q26) MUTATED	36	1	3	0	5	0	1
DEL PEAK 13(6Q26) WILD-TYPE	87	52	44	65	103	66	74

Figure S671. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S672. Gene #64: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 13(6Q26) MUTATED	37	6	2
DEL PEAK 13(6Q26) WILD-TYPE	186	144	155

Figure S672. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S673. Gene #64: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 13(6Q26) MUTATED	16	0	1	28
DEL PEAK 13(6Q26) WILD-TYPE	203	58	136	88

Figure S673. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.001

Table S674. Gene #64: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 13(6Q26) MUTATED	23	13	3
DEL PEAK 13(6Q26) WILD-TYPE	149	83	127

Figure S674. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00021

Table S675. Gene #64: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 13(6Q26) MUTATED	19	1	19
DEL PEAK 13(6Q26) WILD-TYPE	125	114	120

Figure S675. Get High-res Image Gene #64: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S676. Gene #65: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 14(7P22.3) MUTATED	0	8	0	0
DEL PEAK 14(7P22.3) WILD-TYPE	14	9	12	10

Figure S676. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.0022

Table S677. Gene #65: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 14(7P22.3) MUTATED	3	5	0	0	0
DEL PEAK 14(7P22.3) WILD-TYPE	11	4	7	7	16

Figure S677. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S678. Gene #65: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 14(7P22.3) MUTATED	65	4	1	1	1
DEL PEAK 14(7P22.3) WILD-TYPE	104	301	18	8	36

Figure S678. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S679. Gene #65: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 14(7P22.3) MUTATED	45	13	4
DEL PEAK 14(7P22.3) WILD-TYPE	120	76	167

Figure S679. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S680. Gene #65: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 14(7P22.3) MUTATED	5	10	42
DEL PEAK 14(7P22.3) WILD-TYPE	120	141	115

Figure S680. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S681. Gene #65: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 14(7P22.3) MUTATED	2	38	9	8
DEL PEAK 14(7P22.3) WILD-TYPE	106	144	84	42

Figure S681. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S682. Gene #65: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 14(7P22.3) MUTATED	66	2	4
DEL PEAK 14(7P22.3) WILD-TYPE	168	151	146

Figure S682. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S683. Gene #65: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 14(7P22.3) MUTATED	51	0	9	0	8	4	0
DEL PEAK 14(7P22.3) WILD-TYPE	72	53	38	65	100	62	75

Figure S683. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S684. Gene #65: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 14(7P22.3) MUTATED	57	8	5
DEL PEAK 14(7P22.3) WILD-TYPE	166	142	152

Figure S684. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S685. Gene #65: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 14(7P22.3) MUTATED	23	0	2	45
DEL PEAK 14(7P22.3) WILD-TYPE	196	58	135	71

Figure S685. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00027

Table S686. Gene #65: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 14(7P22.3) MUTATED	34	18	6
DEL PEAK 14(7P22.3) WILD-TYPE	138	78	124

Figure S686. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S687. Gene #65: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 14(7P22.3) MUTATED	33	4	21
DEL PEAK 14(7P22.3) WILD-TYPE	111	111	118

Figure S687. Get High-res Image Gene #65: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S688. Gene #66: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 15(7Q11.22) MUTATED	39	0	0	1	1
DEL PEAK 15(7Q11.22) WILD-TYPE	130	305	19	8	36

Figure S688. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S689. Gene #66: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 15(7Q11.22) MUTATED	27	8	3
DEL PEAK 15(7Q11.22) WILD-TYPE	138	81	168

Figure S689. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q11.22' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S690. Gene #66: 'del_7q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 15(7Q11.22) MUTATED	2	4	27
DEL PEAK 15(7Q11.22) WILD-TYPE	123	147	130

Figure S690. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q11.22' versus 'RPPA_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.003

Table S691. Gene #66: 'del_7q11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 15(7Q11.22) MUTATED	1	22	7	3
DEL PEAK 15(7Q11.22) WILD-TYPE	107	160	86	47

Figure S691. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S692. Gene #66: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 15(7Q11.22) MUTATED	39	0	2
DEL PEAK 15(7Q11.22) WILD-TYPE	195	153	148

Figure S692. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S693. Gene #66: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 15(7Q11.22) MUTATED	27	0	4	0	7	3	0
DEL PEAK 15(7Q11.22) WILD-TYPE	96	53	43	65	101	63	75

Figure S693. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S694. Gene #66: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 15(7Q11.22) MUTATED	33	4	3
DEL PEAK 15(7Q11.22) WILD-TYPE	190	146	154

Figure S694. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q11.22' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S695. Gene #66: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 15(7Q11.22) MUTATED	15	0	2	23
DEL PEAK 15(7Q11.22) WILD-TYPE	204	58	135	93

Figure S695. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q11.22' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00771 (Fisher's exact test), Q value = 0.0093

Table S696. Gene #66: 'del_7q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 15(7Q11.22) MUTATED	24	7	5
DEL PEAK 15(7Q11.22) WILD-TYPE	148	89	125

Figure S696. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q11.22' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0017

Table S697. Gene #66: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 15(7Q11.22) MUTATED	22	3	11
DEL PEAK 15(7Q11.22) WILD-TYPE	122	112	128

Figure S697. Get High-res Image Gene #66: 'del_7q11.22' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S698. Gene #67: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 16(7Q31.1) MUTATED	54	0	0	1	0
DEL PEAK 16(7Q31.1) WILD-TYPE	115	305	19	8	37

Figure S698. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S699. Gene #67: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 16(7Q31.1) MUTATED	38	11	1
DEL PEAK 16(7Q31.1) WILD-TYPE	127	78	170

Figure S699. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q31.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S700. Gene #67: 'del_7q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 16(7Q31.1) MUTATED	7	8	33
DEL PEAK 16(7Q31.1) WILD-TYPE	118	143	124

Figure S700. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q31.1' versus 'RPPA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S701. Gene #67: 'del_7q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 16(7Q31.1) MUTATED	1	31	10	6
DEL PEAK 16(7Q31.1) WILD-TYPE	107	151	83	44

Figure S701. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q31.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S702. Gene #67: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 16(7Q31.1) MUTATED	54	0	1
DEL PEAK 16(7Q31.1) WILD-TYPE	180	153	149

Figure S702. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S703. Gene #67: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 16(7Q31.1) MUTATED	44	0	4	0	5	2	0
DEL PEAK 16(7Q31.1) WILD-TYPE	79	53	43	65	103	64	75

Figure S703. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S704. Gene #67: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 16(7Q31.1) MUTATED	48	3	3
DEL PEAK 16(7Q31.1) WILD-TYPE	175	147	154

Figure S704. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S705. Gene #67: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 16(7Q31.1) MUTATED	14	0	2	38
DEL PEAK 16(7Q31.1) WILD-TYPE	205	58	135	78

Figure S705. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00038

Table S706. Gene #67: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 16(7Q31.1) MUTATED	32	10	5
DEL PEAK 16(7Q31.1) WILD-TYPE	140	86	125

Figure S706. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00043 (Fisher's exact test), Q value = 0.00059

Table S707. Gene #67: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 16(7Q31.1) MUTATED	27	4	16
DEL PEAK 16(7Q31.1) WILD-TYPE	117	111	123

Figure S707. Get High-res Image Gene #67: 'del_7q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S708. Gene #68: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 17(7Q36.1) MUTATED	60	1	0	1	1
DEL PEAK 17(7Q36.1) WILD-TYPE	109	304	19	8	36

Figure S708. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S709. Gene #68: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 17(7Q36.1) MUTATED	41	12	1
DEL PEAK 17(7Q36.1) WILD-TYPE	124	77	170

Figure S709. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7q36.1' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S710. Gene #68: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 17(7Q36.1) MUTATED	7	10	35
DEL PEAK 17(7Q36.1) WILD-TYPE	118	141	122

Figure S710. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_7q36.1' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S711. Gene #68: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 17(7Q36.1) MUTATED	1	35	11	5
DEL PEAK 17(7Q36.1) WILD-TYPE	107	147	82	45

Figure S711. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S712. Gene #68: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 17(7Q36.1) MUTATED	62	0	1
DEL PEAK 17(7Q36.1) WILD-TYPE	172	153	149

Figure S712. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S713. Gene #68: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 17(7Q36.1) MUTATED	50	0	7	0	4	2	0
DEL PEAK 17(7Q36.1) WILD-TYPE	73	53	40	65	104	64	75

Figure S713. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S714. Gene #68: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 17(7Q36.1) MUTATED	55	4	3
DEL PEAK 17(7Q36.1) WILD-TYPE	168	146	154

Figure S714. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S715. Gene #68: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 17(7Q36.1) MUTATED	15	0	2	45
DEL PEAK 17(7Q36.1) WILD-TYPE	204	58	135	71

Figure S715. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00015

Table S716. Gene #68: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 17(7Q36.1) MUTATED	34	11	5
DEL PEAK 17(7Q36.1) WILD-TYPE	138	85	125

Figure S716. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S717. Gene #68: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 17(7Q36.1) MUTATED	31	3	16
DEL PEAK 17(7Q36.1) WILD-TYPE	113	112	123

Figure S717. Get High-res Image Gene #68: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 0.00219 (Fisher's exact test), Q value = 0.0028

Table S718. Gene #69: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 18(8P23.2) MUTATED	0	6	0	0
DEL PEAK 18(8P23.2) WILD-TYPE	14	11	12	10

Figure S718. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S719. Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 18(8P23.2) MUTATED	0	6	0	0	0
DEL PEAK 18(8P23.2) WILD-TYPE	14	3	7	7	16

Figure S719. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S720. Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 18(8P23.2) MUTATED	107	7	4	1	0
DEL PEAK 18(8P23.2) WILD-TYPE	62	298	15	8	37

Figure S720. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S721. Gene #69: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 18(8P23.2) MUTATED	84	16	5
DEL PEAK 18(8P23.2) WILD-TYPE	81	73	166

Figure S721. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S722. Gene #69: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 18(8P23.2) MUTATED	13	21	64
DEL PEAK 18(8P23.2) WILD-TYPE	112	130	93

Figure S722. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S723. Gene #69: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 18(8P23.2) MUTATED	3	62	21	12
DEL PEAK 18(8P23.2) WILD-TYPE	105	120	72	38

Figure S723. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S724. Gene #69: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 18(8P23.2) MUTATED	108	5	5
DEL PEAK 18(8P23.2) WILD-TYPE	126	148	145

Figure S724. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S725. Gene #69: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 18(8P23.2) MUTATED	77	0	20	1	14	5	1
DEL PEAK 18(8P23.2) WILD-TYPE	46	53	27	64	94	61	74

Figure S725. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S726. Gene #69: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 18(8P23.2) MUTATED	102	7	7
DEL PEAK 18(8P23.2) WILD-TYPE	121	143	150

Figure S726. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S727. Gene #69: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 18(8P23.2) MUTATED	36	1	5	74
DEL PEAK 18(8P23.2) WILD-TYPE	183	57	132	42

Figure S727. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S728. Gene #69: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 18(8P23.2) MUTATED	68	22	9
DEL PEAK 18(8P23.2) WILD-TYPE	104	74	121

Figure S728. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S729. Gene #69: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 18(8P23.2) MUTATED	61	4	34
DEL PEAK 18(8P23.2) WILD-TYPE	83	111	105

Figure S729. Get High-res Image Gene #69: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p21.2' versus 'MRNA_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0025

Table S730. Gene #70: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 19(8P21.2) MUTATED	0	6	0	0
DEL PEAK 19(8P21.2) WILD-TYPE	14	11	12	10

Figure S730. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S731. Gene #70: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 19(8P21.2) MUTATED	0	6	0	0	0
DEL PEAK 19(8P21.2) WILD-TYPE	14	3	7	7	16

Figure S731. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S732. Gene #70: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 19(8P21.2) MUTATED	109	4	3	1	0
DEL PEAK 19(8P21.2) WILD-TYPE	60	301	16	8	37

Figure S732. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S733. Gene #70: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 19(8P21.2) MUTATED	86	15	2
DEL PEAK 19(8P21.2) WILD-TYPE	79	74	169

Figure S733. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S734. Gene #70: 'del_8p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 19(8P21.2) MUTATED	11	21	62
DEL PEAK 19(8P21.2) WILD-TYPE	114	130	95

Figure S734. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_8p21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S735. Gene #70: 'del_8p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 19(8P21.2) MUTATED	1	62	20	11
DEL PEAK 19(8P21.2) WILD-TYPE	107	120	73	39

Figure S735. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S736. Gene #70: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 19(8P21.2) MUTATED	110	4	2
DEL PEAK 19(8P21.2) WILD-TYPE	124	149	148

Figure S736. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S737. Gene #70: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 19(8P21.2) MUTATED	80	0	20	1	12	3	0
DEL PEAK 19(8P21.2) WILD-TYPE	43	53	27	64	96	63	75

Figure S737. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S738. Gene #70: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 19(8P21.2) MUTATED	104	7	3
DEL PEAK 19(8P21.2) WILD-TYPE	119	143	154

Figure S738. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S739. Gene #70: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 19(8P21.2) MUTATED	32	1	2	79
DEL PEAK 19(8P21.2) WILD-TYPE	187	57	135	37

Figure S739. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S740. Gene #70: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 19(8P21.2) MUTATED	68	23	7
DEL PEAK 19(8P21.2) WILD-TYPE	104	73	123

Figure S740. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S741. Gene #70: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 19(8P21.2) MUTATED	62	2	34
DEL PEAK 19(8P21.2) WILD-TYPE	82	113	105

Figure S741. Get High-res Image Gene #70: 'del_8p21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.033

Table S742. Gene #71: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 20(9P23) MUTATED	1	3	0	0	0
DEL PEAK 20(9P23) WILD-TYPE	13	6	7	7	16

Figure S742. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S743. Gene #71: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 20(9P23) MUTATED	67	2	5	1	4
DEL PEAK 20(9P23) WILD-TYPE	102	303	14	8	33

Figure S743. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S744. Gene #71: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 20(9P23) MUTATED	44	18	8
DEL PEAK 20(9P23) WILD-TYPE	121	71	163

Figure S744. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CNMF'

P value = 0.00255 (Fisher's exact test), Q value = 0.0032

Table S745. Gene #71: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 20(9P23) MUTATED	10	17	34
DEL PEAK 20(9P23) WILD-TYPE	115	134	123

Figure S745. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0011

Table S746. Gene #71: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 20(9P23) MUTATED	4	36	14	7
DEL PEAK 20(9P23) WILD-TYPE	104	146	79	43

Figure S746. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S747. Gene #71: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 20(9P23) MUTATED	63	5	11
DEL PEAK 20(9P23) WILD-TYPE	171	148	139

Figure S747. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S748. Gene #71: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 20(9P23) MUTATED	41	0	14	2	12	9	1
DEL PEAK 20(9P23) WILD-TYPE	82	53	33	63	96	57	74

Figure S748. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S749. Gene #71: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 20(9P23) MUTATED	56	8	14
DEL PEAK 20(9P23) WILD-TYPE	167	142	143

Figure S749. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S750. Gene #71: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 20(9P23) MUTATED	25	0	10	43
DEL PEAK 20(9P23) WILD-TYPE	194	58	127	73

Figure S750. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.026

Table S751. Gene #71: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 20(9P23) MUTATED	37	18	13
DEL PEAK 20(9P23) WILD-TYPE	135	78	117

Figure S751. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00683 (Fisher's exact test), Q value = 0.0083

Table S752. Gene #71: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 20(9P23) MUTATED	35	11	22
DEL PEAK 20(9P23) WILD-TYPE	109	104	117

Figure S752. Get High-res Image Gene #71: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.2' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S753. Gene #72: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 21(9Q21.2) MUTATED	0	9	0	0
DEL PEAK 21(9Q21.2) WILD-TYPE	14	8	12	10

Figure S753. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S754. Gene #72: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 21(9Q21.2) MUTATED	2	7	0	0	0
DEL PEAK 21(9Q21.2) WILD-TYPE	12	2	7	7	16

Figure S754. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S755. Gene #72: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 21(9Q21.2) MUTATED	112	3	7	2	5
DEL PEAK 21(9Q21.2) WILD-TYPE	57	302	12	7	32

Figure S755. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S756. Gene #72: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 21(9Q21.2) MUTATED	78	20	15
DEL PEAK 21(9Q21.2) WILD-TYPE	87	69	156

Figure S756. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S757. Gene #72: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 21(9Q21.2) MUTATED	16	23	60
DEL PEAK 21(9Q21.2) WILD-TYPE	109	128	97

Figure S757. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S758. Gene #72: 'del_9q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 21(9Q21.2) MUTATED	7	64	20	8
DEL PEAK 21(9Q21.2) WILD-TYPE	101	118	73	42

Figure S758. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S759. Gene #72: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 21(9Q21.2) MUTATED	105	8	16
DEL PEAK 21(9Q21.2) WILD-TYPE	129	145	134

Figure S759. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S760. Gene #72: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 21(9Q21.2) MUTATED	77	0	16	3	19	13	1
DEL PEAK 21(9Q21.2) WILD-TYPE	46	53	31	62	89	53	74

Figure S760. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S761. Gene #72: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 21(9Q21.2) MUTATED	93	16	17
DEL PEAK 21(9Q21.2) WILD-TYPE	130	134	140

Figure S761. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S762. Gene #72: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 21(9Q21.2) MUTATED	47	1	13	65
DEL PEAK 21(9Q21.2) WILD-TYPE	172	57	124	51

Figure S762. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 4e-04

Table S763. Gene #72: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 21(9Q21.2) MUTATED	61	29	20
DEL PEAK 21(9Q21.2) WILD-TYPE	111	67	110

Figure S763. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S764. Gene #72: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 21(9Q21.2) MUTATED	61	16	33
DEL PEAK 21(9Q21.2) WILD-TYPE	83	99	106

Figure S764. Get High-res Image Gene #72: 'del_9q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S765. Gene #73: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 22(9Q34.2) MUTATED	0	9	0	0
DEL PEAK 22(9Q34.2) WILD-TYPE	14	8	12	10

Figure S765. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S766. Gene #73: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 22(9Q34.2) MUTATED	2	7	0	0	0
DEL PEAK 22(9Q34.2) WILD-TYPE	12	2	7	7	16

Figure S766. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S767. Gene #73: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 22(9Q34.2) MUTATED	117	4	6	1	4
DEL PEAK 22(9Q34.2) WILD-TYPE	52	301	13	8	33

Figure S767. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S768. Gene #73: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 22(9Q34.2) MUTATED	78	23	13
DEL PEAK 22(9Q34.2) WILD-TYPE	87	66	158

Figure S768. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S769. Gene #73: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 22(9Q34.2) MUTATED	16	27	60
DEL PEAK 22(9Q34.2) WILD-TYPE	109	124	97

Figure S769. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S770. Gene #73: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 22(9Q34.2) MUTATED	7	64	25	7
DEL PEAK 22(9Q34.2) WILD-TYPE	101	118	68	43

Figure S770. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S771. Gene #73: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 22(9Q34.2) MUTATED	106	8	17
DEL PEAK 22(9Q34.2) WILD-TYPE	128	145	133

Figure S771. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S772. Gene #73: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 22(9Q34.2) MUTATED	75	0	16	3	22	14	1
DEL PEAK 22(9Q34.2) WILD-TYPE	48	53	31	62	86	52	74

Figure S772. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S773. Gene #73: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 22(9Q34.2) MUTATED	96	15	18
DEL PEAK 22(9Q34.2) WILD-TYPE	127	135	139

Figure S773. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S774. Gene #73: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 22(9Q34.2) MUTATED	48	1	13	67
DEL PEAK 22(9Q34.2) WILD-TYPE	171	57	124	49

Figure S774. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00031

Table S775. Gene #73: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 22(9Q34.2) MUTATED	64	27	20
DEL PEAK 22(9Q34.2) WILD-TYPE	108	69	110

Figure S775. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S776. Gene #73: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 22(9Q34.2) MUTATED	65	17	29
DEL PEAK 22(9Q34.2) WILD-TYPE	79	98	110

Figure S776. Get High-res Image Gene #73: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S777. Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 23(10Q23.31) MUTATED	70	5	2	0	0
DEL PEAK 23(10Q23.31) WILD-TYPE	99	300	17	9	37

Figure S777. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S778. Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 23(10Q23.31) MUTATED	49	13	6
DEL PEAK 23(10Q23.31) WILD-TYPE	116	76	165

Figure S778. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S779. Gene #74: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 23(10Q23.31) MUTATED	8	15	38
DEL PEAK 23(10Q23.31) WILD-TYPE	117	136	119

Figure S779. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S780. Gene #74: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 23(10Q23.31) MUTATED	3	39	14	5
DEL PEAK 23(10Q23.31) WILD-TYPE	105	143	79	45

Figure S780. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S781. Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 23(10Q23.31) MUTATED	64	4	8
DEL PEAK 23(10Q23.31) WILD-TYPE	170	149	142

Figure S781. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S782. Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 23(10Q23.31) MUTATED	47	0	7	3	12	5	2
DEL PEAK 23(10Q23.31) WILD-TYPE	76	53	40	62	96	61	73

Figure S782. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S783. Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 23(10Q23.31) MUTATED	61	7	8
DEL PEAK 23(10Q23.31) WILD-TYPE	162	143	149

Figure S783. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S784. Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 23(10Q23.31) MUTATED	30	0	7	39
DEL PEAK 23(10Q23.31) WILD-TYPE	189	58	130	77

Figure S784. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.00075

Table S785. Gene #74: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 23(10Q23.31) MUTATED	43	12	12
DEL PEAK 23(10Q23.31) WILD-TYPE	129	84	118

Figure S785. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S786. Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 23(10Q23.31) MUTATED	41	7	19
DEL PEAK 23(10Q23.31) WILD-TYPE	103	108	120

Figure S786. Get High-res Image Gene #74: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S787. Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 24(11P15.5) MUTATED	94	1	6	4	1
DEL PEAK 24(11P15.5) WILD-TYPE	75	304	13	5	36

Figure S787. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S788. Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 24(11P15.5) MUTATED	74	17	6
DEL PEAK 24(11P15.5) WILD-TYPE	91	72	165

Figure S788. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S789. Gene #75: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 24(11P15.5) MUTATED	9	20	52
DEL PEAK 24(11P15.5) WILD-TYPE	116	131	105

Figure S789. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S790. Gene #75: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 24(11P15.5) MUTATED	5	55	14	7
DEL PEAK 24(11P15.5) WILD-TYPE	103	127	79	43

Figure S790. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S791. Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 24(11P15.5) MUTATED	90	3	12
DEL PEAK 24(11P15.5) WILD-TYPE	144	150	138

Figure S791. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S792. Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 24(11P15.5) MUTATED	61	1	18	0	14	9	2
DEL PEAK 24(11P15.5) WILD-TYPE	62	52	29	65	94	57	73

Figure S792. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S793. Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 24(11P15.5) MUTATED	83	9	13
DEL PEAK 24(11P15.5) WILD-TYPE	140	141	144

Figure S793. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S794. Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 24(11P15.5) MUTATED	33	1	11	60
DEL PEAK 24(11P15.5) WILD-TYPE	186	57	126	56

Figure S794. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S795. Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 24(11P15.5) MUTATED	66	18	13
DEL PEAK 24(11P15.5) WILD-TYPE	106	78	117

Figure S795. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S796. Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 24(11P15.5) MUTATED	62	12	23
DEL PEAK 24(11P15.5) WILD-TYPE	82	103	116

Figure S796. Get High-res Image Gene #75: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S797. Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 25(11Q14.1) MUTATED	61	0	4	4	1
DEL PEAK 25(11Q14.1) WILD-TYPE	108	305	15	5	36

Figure S797. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q14.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S798. Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 25(11Q14.1) MUTATED	51	10	5
DEL PEAK 25(11Q14.1) WILD-TYPE	114	79	166

Figure S798. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q14.1' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00013

Table S799. Gene #76: 'del_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 25(11Q14.1) MUTATED	5	19	32
DEL PEAK 25(11Q14.1) WILD-TYPE	120	132	125

Figure S799. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q14.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S800. Gene #76: 'del_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 25(11Q14.1) MUTATED	3	44	7	2
DEL PEAK 25(11Q14.1) WILD-TYPE	105	138	86	48

Figure S800. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S801. Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 25(11Q14.1) MUTATED	60	2	7
DEL PEAK 25(11Q14.1) WILD-TYPE	174	151	143

Figure S801. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S802. Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 25(11Q14.1) MUTATED	43	1	12	1	8	4	0
DEL PEAK 25(11Q14.1) WILD-TYPE	80	52	35	64	100	62	75

Figure S802. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S803. Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 25(11Q14.1) MUTATED	55	7	8
DEL PEAK 25(11Q14.1) WILD-TYPE	168	143	149

Figure S803. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S804. Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 25(11Q14.1) MUTATED	22	0	6	42
DEL PEAK 25(11Q14.1) WILD-TYPE	197	58	131	74

Figure S804. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S805. Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 25(11Q14.1) MUTATED	46	12	7
DEL PEAK 25(11Q14.1) WILD-TYPE	126	84	123

Figure S805. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S806. Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 25(11Q14.1) MUTATED	42	6	17
DEL PEAK 25(11Q14.1) WILD-TYPE	102	109	122

Figure S806. Get High-res Image Gene #76: 'del_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S807. Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 26(11Q25) MUTATED	77	3	6	4	3
DEL PEAK 26(11Q25) WILD-TYPE	92	302	13	5	34

Figure S807. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S808. Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 26(11Q25) MUTATED	66	11	7
DEL PEAK 26(11Q25) WILD-TYPE	99	78	164

Figure S808. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S809. Gene #77: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 26(11Q25) MUTATED	9	22	45
DEL PEAK 26(11Q25) WILD-TYPE	116	129	112

Figure S809. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11q25' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S810. Gene #77: 'del_11q25' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 26(11Q25) MUTATED	5	55	13	3
DEL PEAK 26(11Q25) WILD-TYPE	103	127	80	47

Figure S810. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S811. Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 26(11Q25) MUTATED	76	6	10
DEL PEAK 26(11Q25) WILD-TYPE	158	147	140

Figure S811. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q25' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S812. Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 26(11Q25) MUTATED	52	1	14	2	16	6	1
DEL PEAK 26(11Q25) WILD-TYPE	71	52	33	63	92	60	74

Figure S812. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S813. Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 26(11Q25) MUTATED	67	12	12
DEL PEAK 26(11Q25) WILD-TYPE	156	138	145

Figure S813. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11q25' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S814. Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 26(11Q25) MUTATED	37	0	7	47
DEL PEAK 26(11Q25) WILD-TYPE	182	58	130	69

Figure S814. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S815. Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 26(11Q25) MUTATED	53	18	11
DEL PEAK 26(11Q25) WILD-TYPE	119	78	119

Figure S815. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q25' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S816. Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 26(11Q25) MUTATED	49	8	25
DEL PEAK 26(11Q25) WILD-TYPE	95	107	114

Figure S816. Get High-res Image Gene #77: 'del_11q25' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S817. Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 27(12Q23.1) MUTATED	54	0	1	0	1
DEL PEAK 27(12Q23.1) WILD-TYPE	115	305	18	9	36

Figure S817. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S818. Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 27(12Q23.1) MUTATED	42	6	0
DEL PEAK 27(12Q23.1) WILD-TYPE	123	83	171

Figure S818. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S819. Gene #78: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 27(12Q23.1) MUTATED	4	14	30
DEL PEAK 27(12Q23.1) WILD-TYPE	121	137	127

Figure S819. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S820. Gene #78: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 27(12Q23.1) MUTATED	0	32	10	6
DEL PEAK 27(12Q23.1) WILD-TYPE	108	150	83	44

Figure S820. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S821. Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 27(12Q23.1) MUTATED	51	1	4
DEL PEAK 27(12Q23.1) WILD-TYPE	183	152	146

Figure S821. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S822. Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 27(12Q23.1) MUTATED	39	0	9	0	3	5	0
DEL PEAK 27(12Q23.1) WILD-TYPE	84	53	38	65	105	61	75

Figure S822. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S823. Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 27(12Q23.1) MUTATED	46	6	2
DEL PEAK 27(12Q23.1) WILD-TYPE	177	144	155

Figure S823. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S824. Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 27(12Q23.1) MUTATED	19	0	0	35
DEL PEAK 27(12Q23.1) WILD-TYPE	200	58	137	81

Figure S824. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00012

Table S825. Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 27(12Q23.1) MUTATED	32	11	4
DEL PEAK 27(12Q23.1) WILD-TYPE	140	85	126

Figure S825. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S826. Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 27(12Q23.1) MUTATED	30	2	15
DEL PEAK 27(12Q23.1) WILD-TYPE	114	113	124

Figure S826. Get High-res Image Gene #78: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S827. Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 28(12Q24.33) MUTATED	63	1	1	0	1
DEL PEAK 28(12Q24.33) WILD-TYPE	106	304	18	9	36

Figure S827. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S828. Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 28(12Q24.33) MUTATED	50	8	3
DEL PEAK 28(12Q24.33) WILD-TYPE	115	81	168

Figure S828. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S829. Gene #79: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 28(12Q24.33) MUTATED	5	11	37
DEL PEAK 28(12Q24.33) WILD-TYPE	120	140	120

Figure S829. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S830. Gene #79: 'del_12q24.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 28(12Q24.33) MUTATED	0	36	12	5
DEL PEAK 28(12Q24.33) WILD-TYPE	108	146	81	45

Figure S830. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S831. Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 28(12Q24.33) MUTATED	62	1	3
DEL PEAK 28(12Q24.33) WILD-TYPE	172	152	147

Figure S831. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S832. Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 28(12Q24.33) MUTATED	45	0	8	0	9	4	0
DEL PEAK 28(12Q24.33) WILD-TYPE	78	53	39	65	99	62	75

Figure S832. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S833. Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 28(12Q24.33) MUTATED	55	6	3
DEL PEAK 28(12Q24.33) WILD-TYPE	168	144	154

Figure S833. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S834. Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 28(12Q24.33) MUTATED	23	0	2	39
DEL PEAK 28(12Q24.33) WILD-TYPE	196	58	135	77

Figure S834. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S835. Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 28(12Q24.33) MUTATED	40	12	7
DEL PEAK 28(12Q24.33) WILD-TYPE	132	84	123

Figure S835. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S836. Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 28(12Q24.33) MUTATED	37	4	18
DEL PEAK 28(12Q24.33) WILD-TYPE	107	111	121

Figure S836. Get High-res Image Gene #79: 'del_12q24.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q11' versus 'MRNA_CHIERARCHICAL'

P value = 0.0397 (Fisher's exact test), Q value = 0.045

Table S837. Gene #80: 'del_13q11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 29(13Q11) MUTATED	3	3	0	0	0
DEL PEAK 29(13Q11) WILD-TYPE	11	6	7	7	16

Figure S837. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S838. Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 29(13Q11) MUTATED	80	3	6	3	6
DEL PEAK 29(13Q11) WILD-TYPE	89	302	13	6	31

Figure S838. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S839. Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 29(13Q11) MUTATED	57	17	10
DEL PEAK 29(13Q11) WILD-TYPE	108	72	161

Figure S839. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q11' versus 'RPPA_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0011

Table S840. Gene #80: 'del_13q11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 29(13Q11) MUTATED	12	21	41
DEL PEAK 29(13Q11) WILD-TYPE	113	130	116

Figure S840. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q11' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S841. Gene #80: 'del_13q11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 29(13Q11) MUTATED	4	45	17	8
DEL PEAK 29(13Q11) WILD-TYPE	104	137	76	42

Figure S841. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S842. Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 29(13Q11) MUTATED	76	6	16
DEL PEAK 29(13Q11) WILD-TYPE	158	147	134

Figure S842. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S843. Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 29(13Q11) MUTATED	52	1	11	0	21	12	1
DEL PEAK 29(13Q11) WILD-TYPE	71	52	36	65	87	54	74

Figure S843. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S844. Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 29(13Q11) MUTATED	71	13	13
DEL PEAK 29(13Q11) WILD-TYPE	152	137	144

Figure S844. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S845. Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 29(13Q11) MUTATED	41	1	10	45
DEL PEAK 29(13Q11) WILD-TYPE	178	57	127	71

Figure S845. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.028

Table S846. Gene #80: 'del_13q11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 29(13Q11) MUTATED	42	24	17
DEL PEAK 29(13Q11) WILD-TYPE	130	72	113

Figure S846. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00728 (Fisher's exact test), Q value = 0.0089

Table S847. Gene #80: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 29(13Q11) MUTATED	38	13	32
DEL PEAK 29(13Q11) WILD-TYPE	106	102	107

Figure S847. Get High-res Image Gene #80: 'del_13q11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S848. Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 30(13Q14.2) MUTATED	86	5	8	3	5
DEL PEAK 30(13Q14.2) WILD-TYPE	83	300	11	6	32

Figure S848. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S849. Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 30(13Q14.2) MUTATED	60	20	14
DEL PEAK 30(13Q14.2) WILD-TYPE	105	69	157

Figure S849. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 4e-04

Table S850. Gene #81: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 30(13Q14.2) MUTATED	12	27	45
DEL PEAK 30(13Q14.2) WILD-TYPE	113	124	112

Figure S850. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S851. Gene #81: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 30(13Q14.2) MUTATED	6	50	19	9
DEL PEAK 30(13Q14.2) WILD-TYPE	102	132	74	41

Figure S851. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S852. Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 30(13Q14.2) MUTATED	80	8	19
DEL PEAK 30(13Q14.2) WILD-TYPE	154	145	131

Figure S852. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S853. Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 30(13Q14.2) MUTATED	48	3	15	0	25	14	2
DEL PEAK 30(13Q14.2) WILD-TYPE	75	50	32	65	83	52	73

Figure S853. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S854. Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 30(13Q14.2) MUTATED	71	18	17
DEL PEAK 30(13Q14.2) WILD-TYPE	152	132	140

Figure S854. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S855. Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 30(13Q14.2) MUTATED	48	2	13	43
DEL PEAK 30(13Q14.2) WILD-TYPE	171	56	124	73

Figure S855. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.022 (Fisher's exact test), Q value = 0.025

Table S856. Gene #81: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 30(13Q14.2) MUTATED	49	25	20
DEL PEAK 30(13Q14.2) WILD-TYPE	123	71	110

Figure S856. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00293 (Fisher's exact test), Q value = 0.0037

Table S857. Gene #81: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 30(13Q14.2) MUTATED	47	17	30
DEL PEAK 30(13Q14.2) WILD-TYPE	97	98	109

Figure S857. Get High-res Image Gene #81: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q13.1' versus 'MRNA_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.0096

Table S858. Gene #82: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 31(14Q13.1) MUTATED	0	5	0	0
DEL PEAK 31(14Q13.1) WILD-TYPE	14	12	12	10

Figure S858. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00546 (Fisher's exact test), Q value = 0.0067

Table S859. Gene #82: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 31(14Q13.1) MUTATED	1	4	0	0	0
DEL PEAK 31(14Q13.1) WILD-TYPE	13	5	7	7	16

Figure S859. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S860. Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 31(14Q13.1) MUTATED	63	2	2	3	3
DEL PEAK 31(14Q13.1) WILD-TYPE	106	303	17	6	34

Figure S860. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S861. Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 31(14Q13.1) MUTATED	51	8	5
DEL PEAK 31(14Q13.1) WILD-TYPE	114	81	166

Figure S861. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q13.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S862. Gene #82: 'del_14q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 31(14Q13.1) MUTATED	6	11	38
DEL PEAK 31(14Q13.1) WILD-TYPE	119	140	119

Figure S862. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S863. Gene #82: 'del_14q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 31(14Q13.1) MUTATED	1	39	8	7
DEL PEAK 31(14Q13.1) WILD-TYPE	107	143	85	43

Figure S863. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S864. Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 31(14Q13.1) MUTATED	62	4	6
DEL PEAK 31(14Q13.1) WILD-TYPE	172	149	144

Figure S864. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S865. Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 31(14Q13.1) MUTATED	50	1	5	1	9	5	1
DEL PEAK 31(14Q13.1) WILD-TYPE	73	52	42	64	99	61	74

Figure S865. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S866. Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 31(14Q13.1) MUTATED	58	10	4
DEL PEAK 31(14Q13.1) WILD-TYPE	165	140	153

Figure S866. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S867. Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 31(14Q13.1) MUTATED	27	0	4	41
DEL PEAK 31(14Q13.1) WILD-TYPE	192	58	133	75

Figure S867. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0015

Table S868. Gene #82: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 31(14Q13.1) MUTATED	37	18	9
DEL PEAK 31(14Q13.1) WILD-TYPE	135	78	121

Figure S868. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S869. Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 31(14Q13.1) MUTATED	38	5	21
DEL PEAK 31(14Q13.1) WILD-TYPE	106	110	118

Figure S869. Get High-res Image Gene #82: 'del_14q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q15.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.012

Table S870. Gene #83: 'del_15q15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 32(15Q15.1) MUTATED	1	4	0	1	0
DEL PEAK 32(15Q15.1) WILD-TYPE	13	5	7	6	16

Figure S870. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S871. Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 32(15Q15.1) MUTATED	119	5	8	5	3
DEL PEAK 32(15Q15.1) WILD-TYPE	50	300	11	4	34

Figure S871. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S872. Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 32(15Q15.1) MUTATED	90	23	12
DEL PEAK 32(15Q15.1) WILD-TYPE	75	66	159

Figure S872. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q15.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S873. Gene #83: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 32(15Q15.1) MUTATED	15	26	70
DEL PEAK 32(15Q15.1) WILD-TYPE	110	125	87

Figure S873. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q15.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S874. Gene #83: 'del_15q15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 32(15Q15.1) MUTATED	6	71	23	11
DEL PEAK 32(15Q15.1) WILD-TYPE	102	111	70	39

Figure S874. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S875. Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 32(15Q15.1) MUTATED	119	9	12
DEL PEAK 32(15Q15.1) WILD-TYPE	115	144	138

Figure S875. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S876. Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 32(15Q15.1) MUTATED	86	1	14	4	25	9	1
DEL PEAK 32(15Q15.1) WILD-TYPE	37	52	33	61	83	57	74

Figure S876. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S877. Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 32(15Q15.1) MUTATED	108	18	12
DEL PEAK 32(15Q15.1) WILD-TYPE	115	132	145

Figure S877. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S878. Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 32(15Q15.1) MUTATED	51	1	9	77
DEL PEAK 32(15Q15.1) WILD-TYPE	168	57	128	39

Figure S878. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S879. Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 32(15Q15.1) MUTATED	70	34	18
DEL PEAK 32(15Q15.1) WILD-TYPE	102	62	112

Figure S879. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S880. Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 32(15Q15.1) MUTATED	67	12	43
DEL PEAK 32(15Q15.1) WILD-TYPE	77	103	96

Figure S880. Get High-res Image Gene #83: 'del_15q15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q23' versus 'MRNA_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0027

Table S881. Gene #84: 'del_15q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 33(15Q23) MUTATED	0	6	0	0
DEL PEAK 33(15Q23) WILD-TYPE	14	11	12	10

Figure S881. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00067

Table S882. Gene #84: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 33(15Q23) MUTATED	1	5	0	0	0
DEL PEAK 33(15Q23) WILD-TYPE	13	4	7	7	16

Figure S882. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S883. Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 33(15Q23) MUTATED	95	4	7	6	3
DEL PEAK 33(15Q23) WILD-TYPE	74	301	12	3	34

Figure S883. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S884. Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 33(15Q23) MUTATED	77	16	8
DEL PEAK 33(15Q23) WILD-TYPE	88	73	163

Figure S884. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S885. Gene #84: 'del_15q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 33(15Q23) MUTATED	11	25	55
DEL PEAK 33(15Q23) WILD-TYPE	114	126	102

Figure S885. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S886. Gene #84: 'del_15q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 33(15Q23) MUTATED	4	57	20	10
DEL PEAK 33(15Q23) WILD-TYPE	104	125	73	40

Figure S886. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S887. Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 33(15Q23) MUTATED	98	8	9
DEL PEAK 33(15Q23) WILD-TYPE	136	145	141

Figure S887. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S888. Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 33(15Q23) MUTATED	75	1	12	2	17	7	1
DEL PEAK 33(15Q23) WILD-TYPE	48	52	35	63	91	59	74

Figure S888. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S889. Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 33(15Q23) MUTATED	88	16	9
DEL PEAK 33(15Q23) WILD-TYPE	135	134	148

Figure S889. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S890. Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 33(15Q23) MUTATED	41	1	6	65
DEL PEAK 33(15Q23) WILD-TYPE	178	57	131	51

Figure S890. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S891. Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 33(15Q23) MUTATED	64	22	12
DEL PEAK 33(15Q23) WILD-TYPE	108	74	118

Figure S891. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S892. Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 33(15Q23) MUTATED	59	7	32
DEL PEAK 33(15Q23) WILD-TYPE	85	108	107

Figure S892. Get High-res Image Gene #84: 'del_15q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16p13.3' versus 'MRNA_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.016

Table S893. Gene #85: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 34(16P13.3) MUTATED	1	6	0	0
DEL PEAK 34(16P13.3) WILD-TYPE	13	11	12	10

Figure S893. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0096 (Fisher's exact test), Q value = 0.011

Table S894. Gene #85: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 34(16P13.3) MUTATED	3	4	0	0	0
DEL PEAK 34(16P13.3) WILD-TYPE	11	5	7	7	16

Figure S894. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S895. Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 34(16P13.3) MUTATED	84	2	3	1	2
DEL PEAK 34(16P13.3) WILD-TYPE	85	303	16	8	35

Figure S895. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S896. Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 34(16P13.3) MUTATED	62	17	4
DEL PEAK 34(16P13.3) WILD-TYPE	103	72	167

Figure S896. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S897. Gene #85: 'del_16p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 34(16P13.3) MUTATED	6	17	53
DEL PEAK 34(16P13.3) WILD-TYPE	119	134	104

Figure S897. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S898. Gene #85: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 34(16P13.3) MUTATED	1	53	15	7
DEL PEAK 34(16P13.3) WILD-TYPE	107	129	78	43

Figure S898. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S899. Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 34(16P13.3) MUTATED	83	2	7
DEL PEAK 34(16P13.3) WILD-TYPE	151	151	143

Figure S899. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S900. Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 34(16P13.3) MUTATED	63	1	9	1	11	6	1
DEL PEAK 34(16P13.3) WILD-TYPE	60	52	38	64	97	60	74

Figure S900. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S901. Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 34(16P13.3) MUTATED	74	9	7
DEL PEAK 34(16P13.3) WILD-TYPE	149	141	150

Figure S901. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S902. Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 34(16P13.3) MUTATED	31	0	5	54
DEL PEAK 34(16P13.3) WILD-TYPE	188	58	132	62

Figure S902. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S903. Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 34(16P13.3) MUTATED	51	21	10
DEL PEAK 34(16P13.3) WILD-TYPE	121	75	120

Figure S903. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S904. Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 34(16P13.3) MUTATED	49	6	27
DEL PEAK 34(16P13.3) WILD-TYPE	95	109	112

Figure S904. Get High-res Image Gene #85: 'del_16p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q21' versus 'MRNA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0012

Table S905. Gene #86: 'del_16q21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 35(16Q21) MUTATED	0	8	1	0
DEL PEAK 35(16Q21) WILD-TYPE	14	9	11	10

Figure S905. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q21' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S906. Gene #86: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 35(16Q21) MUTATED	1	7	0	0	1
DEL PEAK 35(16Q21) WILD-TYPE	13	2	7	7	15

Figure S906. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S907. Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 35(16Q21) MUTATED	128	14	7	1	4
DEL PEAK 35(16Q21) WILD-TYPE	41	291	12	8	33

Figure S907. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S908. Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 35(16Q21) MUTATED	93	26	16
DEL PEAK 35(16Q21) WILD-TYPE	72	63	155

Figure S908. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S909. Gene #86: 'del_16q21' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 35(16Q21) MUTATED	18	25	81
DEL PEAK 35(16Q21) WILD-TYPE	107	126	76

Figure S909. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S910. Gene #86: 'del_16q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 35(16Q21) MUTATED	10	81	22	11
DEL PEAK 35(16Q21) WILD-TYPE	98	101	71	39

Figure S910. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S911. Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 35(16Q21) MUTATED	123	14	16
DEL PEAK 35(16Q21) WILD-TYPE	111	139	134

Figure S911. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S912. Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 35(16Q21) MUTATED	89	7	17	3	22	11	4
DEL PEAK 35(16Q21) WILD-TYPE	34	46	30	62	86	55	71

Figure S912. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S913. Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 35(16Q21) MUTATED	108	25	17
DEL PEAK 35(16Q21) WILD-TYPE	115	125	140

Figure S913. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S914. Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 35(16Q21) MUTATED	54	6	14	76
DEL PEAK 35(16Q21) WILD-TYPE	165	52	123	40

Figure S914. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S915. Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 35(16Q21) MUTATED	78	31	22
DEL PEAK 35(16Q21) WILD-TYPE	94	65	108

Figure S915. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S916. Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 35(16Q21) MUTATED	72	16	43
DEL PEAK 35(16Q21) WILD-TYPE	72	99	96

Figure S916. Get High-res Image Gene #86: 'del_16q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q22.3' versus 'MRNA_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.038

Table S917. Gene #87: 'del_16q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 36(16Q22.3) MUTATED	1	7	2	0
DEL PEAK 36(16Q22.3) WILD-TYPE	13	10	10	10

Figure S917. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.012

Table S918. Gene #87: 'del_16q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 36(16Q22.3) MUTATED	4	5	0	0	1
DEL PEAK 36(16Q22.3) WILD-TYPE	10	4	7	7	15

Figure S918. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S919. Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 36(16Q22.3) MUTATED	129	17	7	1	4
DEL PEAK 36(16Q22.3) WILD-TYPE	40	288	12	8	33

Figure S919. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S920. Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 36(16Q22.3) MUTATED	91	28	19
DEL PEAK 36(16Q22.3) WILD-TYPE	74	61	152

Figure S920. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q22.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S921. Gene #87: 'del_16q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 36(16Q22.3) MUTATED	18	25	80
DEL PEAK 36(16Q22.3) WILD-TYPE	107	126	77

Figure S921. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S922. Gene #87: 'del_16q22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 36(16Q22.3) MUTATED	13	78	22	10
DEL PEAK 36(16Q22.3) WILD-TYPE	95	104	71	40

Figure S922. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S923. Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 36(16Q22.3) MUTATED	125	15	18
DEL PEAK 36(16Q22.3) WILD-TYPE	109	138	132

Figure S923. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S924. Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 36(16Q22.3) MUTATED	88	8	18	3	24	12	5
DEL PEAK 36(16Q22.3) WILD-TYPE	35	45	29	62	84	54	70

Figure S924. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S925. Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 36(16Q22.3) MUTATED	110	25	19
DEL PEAK 36(16Q22.3) WILD-TYPE	113	125	138

Figure S925. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S926. Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 36(16Q22.3) MUTATED	55	6	16	77
DEL PEAK 36(16Q22.3) WILD-TYPE	164	52	121	39

Figure S926. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 7.4e-05

Table S927. Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 36(16Q22.3) MUTATED	75	34	25
DEL PEAK 36(16Q22.3) WILD-TYPE	97	62	105

Figure S927. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S928. Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 36(16Q22.3) MUTATED	68	16	50
DEL PEAK 36(16Q22.3) WILD-TYPE	76	99	89

Figure S928. Get High-res Image Gene #87: 'del_16q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q23.1' versus 'MRNA_CNMF'

P value = 0.00314 (Fisher's exact test), Q value = 0.0039

Table S929. Gene #88: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 37(16Q23.1) MUTATED	1	9	2	0
DEL PEAK 37(16Q23.1) WILD-TYPE	13	8	10	10

Figure S929. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00032

Table S930. Gene #88: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 37(16Q23.1) MUTATED	4	7	0	0	1
DEL PEAK 37(16Q23.1) WILD-TYPE	10	2	7	7	15

Figure S930. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S931. Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 37(16Q23.1) MUTATED	134	19	8	1	4
DEL PEAK 37(16Q23.1) WILD-TYPE	35	286	11	8	33

Figure S931. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S932. Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 37(16Q23.1) MUTATED	96	27	19
DEL PEAK 37(16Q23.1) WILD-TYPE	69	62	152

Figure S932. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S933. Gene #88: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 37(16Q23.1) MUTATED	20	29	83
DEL PEAK 37(16Q23.1) WILD-TYPE	105	122	74

Figure S933. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S934. Gene #88: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 37(16Q23.1) MUTATED	13	84	23	12
DEL PEAK 37(16Q23.1) WILD-TYPE	95	98	70	38

Figure S934. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S935. Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 37(16Q23.1) MUTATED	133	16	17
DEL PEAK 37(16Q23.1) WILD-TYPE	101	137	133

Figure S935. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S936. Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 37(16Q23.1) MUTATED	93	8	20	4	25	11	5
DEL PEAK 37(16Q23.1) WILD-TYPE	30	45	27	61	83	55	70

Figure S936. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S937. Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 37(16Q23.1) MUTATED	118	25	18
DEL PEAK 37(16Q23.1) WILD-TYPE	105	125	139

Figure S937. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S938. Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 37(16Q23.1) MUTATED	55	6	15	85
DEL PEAK 37(16Q23.1) WILD-TYPE	164	52	122	31

Figure S938. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S939. Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 37(16Q23.1) MUTATED	80	35	23
DEL PEAK 37(16Q23.1) WILD-TYPE	92	61	107

Figure S939. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S940. Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 37(16Q23.1) MUTATED	72	15	51
DEL PEAK 37(16Q23.1) WILD-TYPE	72	100	88

Figure S940. Get High-res Image Gene #88: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p13.3' versus 'MRNA_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0011

Table S941. Gene #89: 'del_17p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 38(17P13.3) MUTATED	0	8	1	0
DEL PEAK 38(17P13.3) WILD-TYPE	14	9	11	10

Figure S941. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S942. Gene #89: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 38(17P13.3) MUTATED	1	7	1	0	0
DEL PEAK 38(17P13.3) WILD-TYPE	13	2	6	7	16

Figure S942. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S943. Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 38(17P13.3) MUTATED	109	4	5	1	3
DEL PEAK 38(17P13.3) WILD-TYPE	60	301	14	8	34

Figure S943. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S944. Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 38(17P13.3) MUTATED	71	20	13
DEL PEAK 38(17P13.3) WILD-TYPE	94	69	158

Figure S944. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S945. Gene #89: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 38(17P13.3) MUTATED	15	23	59
DEL PEAK 38(17P13.3) WILD-TYPE	110	128	98

Figure S945. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S946. Gene #89: 'del_17p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 38(17P13.3) MUTATED	4	62	21	10
DEL PEAK 38(17P13.3) WILD-TYPE	104	120	72	40

Figure S946. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S947. Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 38(17P13.3) MUTATED	100	6	15
DEL PEAK 38(17P13.3) WILD-TYPE	134	147	135

Figure S947. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S948. Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 38(17P13.3) MUTATED	79	1	8	3	16	13	1
DEL PEAK 38(17P13.3) WILD-TYPE	44	52	39	62	92	53	74

Figure S948. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S949. Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 38(17P13.3) MUTATED	88	16	15
DEL PEAK 38(17P13.3) WILD-TYPE	135	134	142

Figure S949. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S950. Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 38(17P13.3) MUTATED	46	1	12	60
DEL PEAK 38(17P13.3) WILD-TYPE	173	57	125	56

Figure S950. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S951. Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 38(17P13.3) MUTATED	60	26	14
DEL PEAK 38(17P13.3) WILD-TYPE	112	70	116

Figure S951. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S952. Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 38(17P13.3) MUTATED	53	15	32
DEL PEAK 38(17P13.3) WILD-TYPE	91	100	107

Figure S952. Get High-res Image Gene #89: 'del_17p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'MRNA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.00096

Table S953. Gene #90: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 39(17P11.2) MUTATED	0	8	1	0
DEL PEAK 39(17P11.2) WILD-TYPE	14	9	11	10

Figure S953. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S954. Gene #90: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 39(17P11.2) MUTATED	0	8	1	0	0
DEL PEAK 39(17P11.2) WILD-TYPE	14	1	6	7	16

Figure S954. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S955. Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 39(17P11.2) MUTATED	116	4	4	1	3
DEL PEAK 39(17P11.2) WILD-TYPE	53	301	15	8	34

Figure S955. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S956. Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 39(17P11.2) MUTATED	79	21	12
DEL PEAK 39(17P11.2) WILD-TYPE	86	68	159

Figure S956. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S957. Gene #90: 'del_17p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 39(17P11.2) MUTATED	16	19	61
DEL PEAK 39(17P11.2) WILD-TYPE	109	132	96

Figure S957. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S958. Gene #90: 'del_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 39(17P11.2) MUTATED	4	64	17	11
DEL PEAK 39(17P11.2) WILD-TYPE	104	118	76	39

Figure S958. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S959. Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 39(17P11.2) MUTATED	110	4	14
DEL PEAK 39(17P11.2) WILD-TYPE	124	149	136

Figure S959. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S960. Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 39(17P11.2) MUTATED	85	1	10	2	17	12	1
DEL PEAK 39(17P11.2) WILD-TYPE	38	52	37	63	91	54	74

Figure S960. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S961. Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 39(17P11.2) MUTATED	94	14	16
DEL PEAK 39(17P11.2) WILD-TYPE	129	136	141

Figure S961. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S962. Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 39(17P11.2) MUTATED	45	0	13	66
DEL PEAK 39(17P11.2) WILD-TYPE	174	58	124	50

Figure S962. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S963. Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 39(17P11.2) MUTATED	63	29	15
DEL PEAK 39(17P11.2) WILD-TYPE	109	67	115

Figure S963. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S964. Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 39(17P11.2) MUTATED	57	15	35
DEL PEAK 39(17P11.2) WILD-TYPE	87	100	104

Figure S964. Get High-res Image Gene #90: 'del_17p11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.00086

Table S965. Gene #91: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 40(17Q11.2) MUTATED	0	7	0	0
DEL PEAK 40(17Q11.2) WILD-TYPE	14	10	12	10

Figure S965. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S966. Gene #91: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 40(17Q11.2) MUTATED	0	7	0	0	0
DEL PEAK 40(17Q11.2) WILD-TYPE	14	2	7	7	16

Figure S966. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S967. Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 40(17Q11.2) MUTATED	93	2	5	1	4
DEL PEAK 40(17Q11.2) WILD-TYPE	76	303	14	8	33

Figure S967. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S968. Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 40(17Q11.2) MUTATED	58	18	14
DEL PEAK 40(17Q11.2) WILD-TYPE	107	71	157

Figure S968. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S969. Gene #91: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 40(17Q11.2) MUTATED	11	19	50
DEL PEAK 40(17Q11.2) WILD-TYPE	114	132	107

Figure S969. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S970. Gene #91: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 40(17Q11.2) MUTATED	4	52	16	8
DEL PEAK 40(17Q11.2) WILD-TYPE	104	130	77	42

Figure S970. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S971. Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 40(17Q11.2) MUTATED	84	6	14
DEL PEAK 40(17Q11.2) WILD-TYPE	150	147	136

Figure S971. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S972. Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 40(17Q11.2) MUTATED	62	1	6	3	19	11	2
DEL PEAK 40(17Q11.2) WILD-TYPE	61	52	41	62	89	55	73

Figure S972. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S973. Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 40(17Q11.2) MUTATED	75	10	16
DEL PEAK 40(17Q11.2) WILD-TYPE	148	140	141

Figure S973. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S974. Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 40(17Q11.2) MUTATED	40	1	13	47
DEL PEAK 40(17Q11.2) WILD-TYPE	179	57	124	69

Figure S974. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00386 (Fisher's exact test), Q value = 0.0048

Table S975. Gene #91: 'del_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 40(17Q11.2) MUTATED	50	21	17
DEL PEAK 40(17Q11.2) WILD-TYPE	122	75	113

Figure S975. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00304 (Fisher's exact test), Q value = 0.0038

Table S976. Gene #91: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 40(17Q11.2) MUTATED	44	15	29
DEL PEAK 40(17Q11.2) WILD-TYPE	100	100	110

Figure S976. Get High-res Image Gene #91: 'del_17q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 6e-05

Table S977. Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 41(17Q21.31) MUTATED	0	9	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	14	8	12	10

Figure S977. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S978. Gene #92: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 41(17Q21.31) MUTATED	1	8	0	0	0
DEL PEAK 41(17Q21.31) WILD-TYPE	13	1	7	7	16

Figure S978. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S979. Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 41(17Q21.31) MUTATED	104	1	4	1	4
DEL PEAK 41(17Q21.31) WILD-TYPE	65	304	15	8	33

Figure S979. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S980. Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 41(17Q21.31) MUTATED	64	22	13
DEL PEAK 41(17Q21.31) WILD-TYPE	101	67	158

Figure S980. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S981. Gene #92: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 41(17Q21.31) MUTATED	9	22	57
DEL PEAK 41(17Q21.31) WILD-TYPE	116	129	100

Figure S981. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S982. Gene #92: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 41(17Q21.31) MUTATED	3	59	19	7
DEL PEAK 41(17Q21.31) WILD-TYPE	105	123	74	43

Figure S982. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S983. Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 41(17Q21.31) MUTATED	93	5	15
DEL PEAK 41(17Q21.31) WILD-TYPE	141	148	135

Figure S983. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S984. Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 41(17Q21.31) MUTATED	72	1	6	3	18	12	1
DEL PEAK 41(17Q21.31) WILD-TYPE	51	52	41	62	90	54	74

Figure S984. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S985. Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 41(17Q21.31) MUTATED	78	14	17
DEL PEAK 41(17Q21.31) WILD-TYPE	145	136	140

Figure S985. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S986. Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 41(17Q21.31) MUTATED	41	0	14	54
DEL PEAK 41(17Q21.31) WILD-TYPE	178	58	123	62

Figure S986. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00019

Table S987. Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 41(17Q21.31) MUTATED	58	21	17
DEL PEAK 41(17Q21.31) WILD-TYPE	114	75	113

Figure S987. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.0016

Table S988. Gene #92: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 41(17Q21.31) MUTATED	49	17	30
DEL PEAK 41(17Q21.31) WILD-TYPE	95	98	109

Figure S988. Get High-res Image Gene #92: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S989. Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 42(18Q21.2) MUTATED	74	2	8	4	3
DEL PEAK 42(18Q21.2) WILD-TYPE	95	303	11	5	34

Figure S989. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S990. Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 42(18Q21.2) MUTATED	57	14	10
DEL PEAK 42(18Q21.2) WILD-TYPE	108	75	161

Figure S990. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q21.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S991. Gene #93: 'del_18q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 42(18Q21.2) MUTATED	8	21	49
DEL PEAK 42(18Q21.2) WILD-TYPE	117	130	108

Figure S991. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q21.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S992. Gene #93: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 42(18Q21.2) MUTATED	4	47	19	8
DEL PEAK 42(18Q21.2) WILD-TYPE	104	135	74	42

Figure S992. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S993. Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 42(18Q21.2) MUTATED	75	5	11
DEL PEAK 42(18Q21.2) WILD-TYPE	159	148	139

Figure S993. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S994. Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 42(18Q21.2) MUTATED	41	1	15	1	24	9	0
DEL PEAK 42(18Q21.2) WILD-TYPE	82	52	32	64	84	57	75

Figure S994. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S995. Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 42(18Q21.2) MUTATED	71	8	11
DEL PEAK 42(18Q21.2) WILD-TYPE	152	142	146

Figure S995. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S996. Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 42(18Q21.2) MUTATED	35	0	8	47
DEL PEAK 42(18Q21.2) WILD-TYPE	184	58	129	69

Figure S996. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.0027

Table S997. Gene #93: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 42(18Q21.2) MUTATED	46	19	14
DEL PEAK 42(18Q21.2) WILD-TYPE	126	77	116

Figure S997. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S998. Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 42(18Q21.2) MUTATED	44	10	25
DEL PEAK 42(18Q21.2) WILD-TYPE	100	105	114

Figure S998. Get High-res Image Gene #93: 'del_18q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S999. Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 43(18Q23) MUTATED	80	2	9	3	4
DEL PEAK 43(18Q23) WILD-TYPE	89	303	10	6	33

Figure S999. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1000. Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 43(18Q23) MUTATED	62	14	10
DEL PEAK 43(18Q23) WILD-TYPE	103	75	161

Figure S1000. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1001. Gene #94: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 43(18Q23) MUTATED	9	23	51
DEL PEAK 43(18Q23) WILD-TYPE	116	128	106

Figure S1001. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_18q23' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1002. Gene #94: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 43(18Q23) MUTATED	5	54	19	5
DEL PEAK 43(18Q23) WILD-TYPE	103	128	74	45

Figure S1002. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1003. Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 43(18Q23) MUTATED	82	5	11
DEL PEAK 43(18Q23) WILD-TYPE	152	148	139

Figure S1003. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1004. Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 43(18Q23) MUTATED	46	1	19	1	22	8	1
DEL PEAK 43(18Q23) WILD-TYPE	77	52	28	64	86	58	74

Figure S1004. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1005. Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 43(18Q23) MUTATED	74	10	12
DEL PEAK 43(18Q23) WILD-TYPE	149	140	145

Figure S1005. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1006. Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 43(18Q23) MUTATED	33	1	9	53
DEL PEAK 43(18Q23) WILD-TYPE	186	57	128	63

Figure S1006. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00034

Table S1007. Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 43(18Q23) MUTATED	49	22	13
DEL PEAK 43(18Q23) WILD-TYPE	123	74	117

Figure S1007. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 2e-04

Table S1008. Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 43(18Q23) MUTATED	44	11	29
DEL PEAK 43(18Q23) WILD-TYPE	100	104	110

Figure S1008. Get High-res Image Gene #94: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1009. Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 44(19P13.3) MUTATED	0	11	0	0
DEL PEAK 44(19P13.3) WILD-TYPE	14	6	12	10

Figure S1009. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1010. Gene #95: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 44(19P13.3) MUTATED	2	9	0	0	0
DEL PEAK 44(19P13.3) WILD-TYPE	12	0	7	7	16

Figure S1010. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1011. Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 44(19P13.3) MUTATED	145	0	5	3	1
DEL PEAK 44(19P13.3) WILD-TYPE	24	305	14	6	36

Figure S1011. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1012. Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 44(19P13.3) MUTATED	108	23	5
DEL PEAK 44(19P13.3) WILD-TYPE	57	66	166

Figure S1012. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1013. Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 44(19P13.3) MUTATED	14	31	77
DEL PEAK 44(19P13.3) WILD-TYPE	111	120	80

Figure S1013. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1014. Gene #95: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 44(19P13.3) MUTATED	3	84	24	11
DEL PEAK 44(19P13.3) WILD-TYPE	105	98	69	39

Figure S1014. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1015. Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 44(19P13.3) MUTATED	140	4	9
DEL PEAK 44(19P13.3) WILD-TYPE	94	149	141

Figure S1015. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1016. Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 44(19P13.3) MUTATED	102	1	20	2	21	7	0
DEL PEAK 44(19P13.3) WILD-TYPE	21	52	27	63	87	59	75

Figure S1016. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1017. Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 44(19P13.3) MUTATED	127	12	10
DEL PEAK 44(19P13.3) WILD-TYPE	96	138	147

Figure S1017. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1018. Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 44(19P13.3) MUTATED	45	0	10	94
DEL PEAK 44(19P13.3) WILD-TYPE	174	58	127	22

Figure S1018. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1019. Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 44(19P13.3) MUTATED	83	31	18
DEL PEAK 44(19P13.3) WILD-TYPE	89	65	112

Figure S1019. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1020. Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 44(19P13.3) MUTATED	78	11	43
DEL PEAK 44(19P13.3) WILD-TYPE	66	104	96

Figure S1020. Get High-res Image Gene #95: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1021. Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 45(19P12) MUTATED	50	1	5	1	1
DEL PEAK 45(19P12) WILD-TYPE	119	304	14	8	36

Figure S1021. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1022. Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 45(19P12) MUTATED	38	10	4
DEL PEAK 45(19P12) WILD-TYPE	127	79	167

Figure S1022. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p12' versus 'RPPA_CNMF'

P value = 0.00603 (Fisher's exact test), Q value = 0.0074

Table S1023. Gene #96: 'del_19p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 45(19P12) MUTATED	6	15	26
DEL PEAK 45(19P12) WILD-TYPE	119	136	131

Figure S1023. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1024. Gene #96: 'del_19p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 45(19P12) MUTATED	2	32	12	1
DEL PEAK 45(19P12) WILD-TYPE	106	150	81	49

Figure S1024. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1025. Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 45(19P12) MUTATED	47	5	6
DEL PEAK 45(19P12) WILD-TYPE	187	148	144

Figure S1025. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1026. Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 45(19P12) MUTATED	32	1	9	1	11	4	0
DEL PEAK 45(19P12) WILD-TYPE	91	52	38	64	97	62	75

Figure S1026. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1027. Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 45(19P12) MUTATED	43	9	5
DEL PEAK 45(19P12) WILD-TYPE	180	141	152

Figure S1027. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1028. Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 45(19P12) MUTATED	24	1	4	28
DEL PEAK 45(19P12) WILD-TYPE	195	57	133	88

Figure S1028. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0329 (Fisher's exact test), Q value = 0.037

Table S1029. Gene #96: 'del_19p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 45(19P12) MUTATED	30	10	10
DEL PEAK 45(19P12) WILD-TYPE	142	86	120

Figure S1029. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S1030. Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 45(19P12) MUTATED	32	5	13
DEL PEAK 45(19P12) WILD-TYPE	112	110	126

Figure S1030. Get High-res Image Gene #96: 'del_19p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.43' versus 'MRNA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 9e-04

Table S1031. Gene #97: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 46(19Q13.43) MUTATED	0	8	1	0
DEL PEAK 46(19Q13.43) WILD-TYPE	14	9	11	10

Figure S1031. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.43' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1032. Gene #97: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 46(19Q13.43) MUTATED	1	7	1	0	0
DEL PEAK 46(19Q13.43) WILD-TYPE	13	2	6	7	16

Figure S1032. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.43' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1033. Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 46(19Q13.43) MUTATED	61	1	3	1	1
DEL PEAK 46(19Q13.43) WILD-TYPE	108	304	16	8	36

Figure S1033. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.43' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1034. Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 46(19Q13.43) MUTATED	43	11	2
DEL PEAK 46(19Q13.43) WILD-TYPE	122	78	169

Figure S1034. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.43' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00026

Table S1035. Gene #97: 'del_19q13.43' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 46(19Q13.43) MUTATED	8	10	32
DEL PEAK 46(19Q13.43) WILD-TYPE	117	141	125

Figure S1035. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.43' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1036. Gene #97: 'del_19q13.43' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 46(19Q13.43) MUTATED	1	34	11	4
DEL PEAK 46(19Q13.43) WILD-TYPE	107	148	82	46

Figure S1036. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.43' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1037. Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 46(19Q13.43) MUTATED	59	3	4
DEL PEAK 46(19Q13.43) WILD-TYPE	175	150	146

Figure S1037. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.43' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1038. Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 46(19Q13.43) MUTATED	44	1	8	0	11	2	0
DEL PEAK 46(19Q13.43) WILD-TYPE	79	52	39	65	97	64	75

Figure S1038. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1039. Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 46(19Q13.43) MUTATED	55	4	4
DEL PEAK 46(19Q13.43) WILD-TYPE	168	146	153

Figure S1039. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.43' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1040. Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 46(19Q13.43) MUTATED	27	0	2	34
DEL PEAK 46(19Q13.43) WILD-TYPE	192	58	135	82

Figure S1040. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.43' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00995 (Fisher's exact test), Q value = 0.012

Table S1041. Gene #97: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 46(19Q13.43) MUTATED	32	15	9
DEL PEAK 46(19Q13.43) WILD-TYPE	140	81	121

Figure S1041. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.43' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S1042. Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 46(19Q13.43) MUTATED	29	2	25
DEL PEAK 46(19Q13.43) WILD-TYPE	115	113	114

Figure S1042. Get High-res Image Gene #97: 'del_19q13.43' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1043. Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 47(20P12.1) MUTATED	25	6	2	1	2
DEL PEAK 47(20P12.1) WILD-TYPE	144	299	17	8	35

Figure S1043. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p12.1' versus 'METHLYATION_CNMF'

P value = 0.0424 (Fisher's exact test), Q value = 0.048

Table S1044. Gene #98: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 47(20P12.1) MUTATED	17	5	6
DEL PEAK 47(20P12.1) WILD-TYPE	148	84	165

Figure S1044. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p12.1' versus 'RPPA_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.0032

Table S1045. Gene #98: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 47(20P12.1) MUTATED	5	22	1	2
DEL PEAK 47(20P12.1) WILD-TYPE	103	160	92	48

Figure S1045. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00038

Table S1046. Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 47(20P12.1) MUTATED	27	3	6
DEL PEAK 47(20P12.1) WILD-TYPE	207	150	144

Figure S1046. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00137 (Fisher's exact test), Q value = 0.0018

Table S1047. Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 47(20P12.1) MUTATED	17	3	6	0	6	2	2
DEL PEAK 47(20P12.1) WILD-TYPE	106	50	41	65	102	64	73

Figure S1047. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p12.1' versus 'MIRSEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00072

Table S1048. Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 47(20P12.1) MUTATED	26	5	4
DEL PEAK 47(20P12.1) WILD-TYPE	197	145	153

Figure S1048. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.001

Table S1049. Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 47(20P12.1) MUTATED	10	1	6	18
DEL PEAK 47(20P12.1) WILD-TYPE	209	57	131	98

Figure S1049. Get High-res Image Gene #98: 'del_20p12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 4.6e-05

Table S1050. Gene #99: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 48(22Q13.32) MUTATED	0	9	0	0
DEL PEAK 48(22Q13.32) WILD-TYPE	14	8	12	10

Figure S1050. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 3.1e-05

Table S1051. Gene #99: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 48(22Q13.32) MUTATED	2	7	0	0	0
DEL PEAK 48(22Q13.32) WILD-TYPE	12	2	7	7	16

Figure S1051. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1052. Gene #99: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 48(22Q13.32) MUTATED	122	7	4	5	3
DEL PEAK 48(22Q13.32) WILD-TYPE	47	298	15	4	34

Figure S1052. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1053. Gene #99: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 48(22Q13.32) MUTATED	84	23	18
DEL PEAK 48(22Q13.32) WILD-TYPE	81	66	153

Figure S1053. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1054. Gene #99: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 48(22Q13.32) MUTATED	15	30	68
DEL PEAK 48(22Q13.32) WILD-TYPE	110	121	89

Figure S1054. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1055. Gene #99: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 48(22Q13.32) MUTATED	4	72	24	13
DEL PEAK 48(22Q13.32) WILD-TYPE	104	110	69	37

Figure S1055. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1056. Gene #99: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 48(22Q13.32) MUTATED	113	8	19
DEL PEAK 48(22Q13.32) WILD-TYPE	121	145	131

Figure S1056. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_22q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1057. Gene #99: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 48(22Q13.32) MUTATED	83	1	10	2	26	14	4
DEL PEAK 48(22Q13.32) WILD-TYPE	40	52	37	63	82	52	71

Figure S1057. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1058. Gene #99: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 48(22Q13.32) MUTATED	103	14	20
DEL PEAK 48(22Q13.32) WILD-TYPE	120	136	137

Figure S1058. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1059. Gene #99: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 48(22Q13.32) MUTATED	52	0	17	68
DEL PEAK 48(22Q13.32) WILD-TYPE	167	58	120	48

Figure S1059. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 8.8e-05

Table S1060. Gene #99: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 48(22Q13.32) MUTATED	69	28	22
DEL PEAK 48(22Q13.32) WILD-TYPE	103	68	108

Figure S1060. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1061. Gene #99: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 48(22Q13.32) MUTATED	64	19	36
DEL PEAK 48(22Q13.32) WILD-TYPE	80	96	103

Figure S1061. Get High-res Image Gene #99: 'del_22q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'MRNA_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.00087

Table S1062. Gene #100: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
DEL PEAK 49(XP21.1) MUTATED	0	7	0	0
DEL PEAK 49(XP21.1) WILD-TYPE	14	10	12	10

Figure S1062. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xp21.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00118 (Fisher's exact test), Q value = 0.0015

Table S1063. Gene #100: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
DEL PEAK 49(XP21.1) MUTATED	2	5	0	0	0
DEL PEAK 49(XP21.1) WILD-TYPE	12	4	7	7	16

Figure S1063. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1064. Gene #100: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
DEL PEAK 49(XP21.1) MUTATED	78	2	3	2	3
DEL PEAK 49(XP21.1) WILD-TYPE	91	303	16	7	34

Figure S1064. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1065. Gene #100: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
DEL PEAK 49(XP21.1) MUTATED	54	12	9
DEL PEAK 49(XP21.1) WILD-TYPE	111	77	162

Figure S1065. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1066. Gene #100: 'del_xp21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	125	151	157
DEL PEAK 49(XP21.1) MUTATED	9	18	47
DEL PEAK 49(XP21.1) WILD-TYPE	116	133	110

Figure S1066. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xp21.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1067. Gene #100: 'del_xp21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
DEL PEAK 49(XP21.1) MUTATED	4	51	13	6
DEL PEAK 49(XP21.1) WILD-TYPE	104	131	80	44

Figure S1067. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1068. Gene #100: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
DEL PEAK 49(XP21.1) MUTATED	76	5	6
DEL PEAK 49(XP21.1) WILD-TYPE	158	148	144

Figure S1068. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1069. Gene #100: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
DEL PEAK 49(XP21.1) MUTATED	55	2	10	1	15	4	0
DEL PEAK 49(XP21.1) WILD-TYPE	68	51	37	64	93	62	75

Figure S1069. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1070. Gene #100: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
DEL PEAK 49(XP21.1) MUTATED	65	11	9
DEL PEAK 49(XP21.1) WILD-TYPE	158	139	148

Figure S1070. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1071. Gene #100: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
DEL PEAK 49(XP21.1) MUTATED	34	0	5	46
DEL PEAK 49(XP21.1) WILD-TYPE	185	58	132	70

Figure S1071. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 1e-04

Table S1072. Gene #100: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
DEL PEAK 49(XP21.1) MUTATED	47	17	11
DEL PEAK 49(XP21.1) WILD-TYPE	125	79	119

Figure S1072. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 1.6e-05

Table S1073. Gene #100: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
DEL PEAK 49(XP21.1) MUTATED	44	6	25
DEL PEAK 49(XP21.1) WILD-TYPE	100	109	114

Figure S1073. Get High-res Image Gene #100: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCEC-TP/19782701/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/20144021/UCEC-TP.transferedmergedcluster.txt
Number of patients = 539
Number of significantly focal cnvs = 100
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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