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

Lung Squamous Cell Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1F18Z59

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 83 focal events and 12 molecular subtypes across 501 patients, 544 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2p16.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_2q31.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_3q26.33 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_4q12 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_5p12 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_6p12.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
amp_6q12 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_7p11.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_7q21.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'MRNA_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_9p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12p13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_12q15 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
amp_14q13.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
amp_14q32.33 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
amp_15q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q25.1 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18p11.32 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_18q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.2 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_20p12.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_20q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
amp_22q11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
amp_xq28 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.
del_1p36.11 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_1p13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2p25.3 cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_2q37.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p25.3 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p13 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p12.3 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_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_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q22.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_4q32.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q12.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_5q31.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_6q26 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q11.22 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_7q36.3 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_9q21.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10p15.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_10q23.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_11q22.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_11q25 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_14q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q11.2 cnv correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.
del_15q21.1 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_16p13.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
del_16q23.1 cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p11.2 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_17q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_17q25.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_18q23 cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.
del_19p13.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.32 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
del_21q11.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_21q22.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
del_22q11.21 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_22q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
del_xp22.2 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp11.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xq22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', '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 83 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, 544 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 3q26 33	452 (90%)	49	0.00073 (0.00275)	0.00045 (0.00194)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00072 (0.00273)	0.00847 (0.0207)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00024 (0.00113)
del 1p36 11	228 (46%)	273	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00047 (0.00198)	0.0154 (0.0339)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	6e-05 (0.000349)
del 4q32 3	329 (66%)	172	0.00112 (0.00385)	0.018 (0.0385)	1e-05 (8.16e-05)	0.00685 (0.0174)	0.029 (0.0572)	0.0188 (0.0401)	2e-05 (0.000142)	0.00035 (0.00158)	3e-05 (0.000193)	0.00255 (0.00765)	0.00024 (0.00113)	0.00011 (0.000589)
amp 2p16 1	275 (55%)	226	0.00084 (0.00309)	0.00039 (0.00171)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00797 (0.0196)	0.147 (0.217)	1e-05 (8.16e-05)	2e-05 (0.000142)	1e-05 (8.16e-05)	0.00071 (0.00271)	0.00037 (0.00163)	0.00061 (0.00243)
del 1p13 1	221 (44%)	280	0.00022 (0.00106)	5e-05 (3e-04)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00048 (0.00202)	0.0503 (0.0919)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00014 (0.000719)	0.00047 (0.00198)
del 2q37 1	159 (32%)	342	0.0016 (0.00516)	0.00071 (0.00271)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00499 (0.0132)	0.357 (0.442)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	2e-05 (0.000142)	0.00028 (0.00129)	0.00037 (0.00163)
del 4p15 2	316 (63%)	185	0.00013 (0.000681)	3e-05 (0.000193)	1e-05 (8.16e-05)	0.00027 (0.00126)	0.0285 (0.0564)	0.0449 (0.0832)	7e-05 (0.000401)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0562 (0.101)	0.0008 (0.00296)	0.00062 (0.00245)
del 9q21 11	251 (50%)	250	0.00061 (0.00243)	4e-05 (0.000247)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.138 (0.207)	0.0219 (0.0455)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	2e-05 (0.000142)	1e-05 (8.16e-05)	0.00317 (0.00907)	0.0151 (0.0336)
del 10q23 31	268 (53%)	233	0.00975 (0.0236)	0.00116 (0.00397)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.12 (0.183)	0.0425 (0.0798)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00024 (0.00113)	1e-05 (8.16e-05)	5e-05 (3e-04)	0.0113 (0.0264)
amp 1q21 2	258 (51%)	243	0.0415 (0.0785)	0.0994 (0.158)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0222 (0.046)	0.3 (0.387)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	3e-05 (0.000193)	0.00049 (0.00205)	0.0111 (0.026)
amp 17q25 1	236 (47%)	265	0.00399 (0.011)	0.134 (0.203)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00052 (0.00216)	0.505 (0.582)	3e-05 (0.000193)	3e-05 (0.000193)	0.00064 (0.00252)	0.00473 (0.0126)	0.00065 (0.00255)	0.0251 (0.0508)
del 3p13	434 (87%)	67	0.0439 (0.0819)	0.355 (0.44)	1e-05 (8.16e-05)	2e-05 (0.000142)	0.258 (0.343)	0.0448 (0.0832)	0.0006 (0.00243)	0.0008 (0.00296)	2e-05 (0.000142)	1e-05 (8.16e-05)	2e-05 (0.000142)	0.00146 (0.00477)
del 3p12 3	421 (84%)	80	0.0357 (0.0689)	0.394 (0.48)	1e-05 (8.16e-05)	2e-05 (0.000142)	0.442 (0.522)	0.00751 (0.0187)	0.00216 (0.00665)	0.00757 (0.0188)	0.00159 (0.00514)	3e-05 (0.000193)	9e-05 (0.000501)	0.00369 (0.0104)
del 4q22 1	285 (57%)	216	0.00054 (0.00223)	0.00422 (0.0115)	1e-05 (8.16e-05)	0.0488 (0.0895)	0.0281 (0.0558)	0.15 (0.22)	3e-05 (0.000193)	0.0146 (0.0328)	1e-05 (8.16e-05)	0.00613 (0.0158)	0.00087 (0.00316)	0.322 (0.409)
del 9p23	332 (66%)	169	0.0149 (0.0332)	0.00163 (0.00524)	1e-05 (8.16e-05)	0.00217 (0.00665)	0.555 (0.624)	0.114 (0.176)	0.0001 (0.000544)	0.00099 (0.00348)	0.00089 (0.00321)	0.0002 (0.000981)	1e-05 (8.16e-05)	0.0205 (0.0432)
amp 2q31 2	172 (34%)	329	0.0389 (0.0744)	0.0228 (0.047)	1e-05 (8.16e-05)	0.00108 (0.00375)	0.00928 (0.0225)	0.0783 (0.133)	3e-05 (0.000193)	1e-05 (8.16e-05)	0.00078 (0.00292)	0.256 (0.342)	0.00397 (0.011)	0.0659 (0.115)
amp 7q21 2	264 (53%)	237	0.115 (0.177)	0.0151 (0.0336)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.13 (0.196)	0.976 (0.979)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00098 (0.00346)	0.00269 (0.0079)	0.0419 (0.0788)
amp 11q13 3	185 (37%)	316	0.0416 (0.0785)	0.0341 (0.0662)	0.00165 (0.00525)	0.00017 (0.000847)	0.608 (0.669)	0.177 (0.252)	0.0211 (0.0443)	0.0647 (0.113)	0.0154 (0.0339)	0.00465 (0.0124)	0.00164 (0.00525)	0.0195 (0.0412)
amp 12p13 33	255 (51%)	246	0.00197 (0.00609)	0.0218 (0.0455)	1e-05 (8.16e-05)	0.00371 (0.0104)	0.244 (0.33)	0.745 (0.784)	1e-05 (8.16e-05)	0.0019 (0.0059)	0.0141 (0.0318)	0.00267 (0.00789)	0.00296 (0.00855)	0.0625 (0.11)
amp 18q11 2	151 (30%)	350	0.00069 (0.00267)	0.0157 (0.0342)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0191 (0.0405)	0.473 (0.554)	1e-05 (8.16e-05)	8e-05 (0.000453)	0.0022 (0.00672)	0.00282 (0.00819)	0.0557 (0.1)	0.0586 (0.105)
del 2q22 1	131 (26%)	370	0.0511 (0.0929)	0.336 (0.423)	1e-05 (8.16e-05)	3e-05 (0.000193)	0.0477 (0.0878)	0.0998 (0.159)	0.00257 (0.00766)	0.00713 (0.0179)	0.00165 (0.00525)	0.00051 (0.00213)	0.00071 (0.00271)	0.0064 (0.0164)
del 3p25 3	398 (79%)	103	0.0402 (0.0766)	0.202 (0.28)	2e-05 (0.000142)	0.00023 (0.0011)	0.321 (0.408)	0.283 (0.369)	0.00271 (0.00794)	0.00032 (0.00146)	0.00444 (0.012)	0.00014 (0.000719)	0.0115 (0.0267)	0.024 (0.0492)
del 3p12 3	427 (85%)	74	0.0683 (0.118)	0.227 (0.31)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.532 (0.604)	0.00577 (0.015)	0.00061 (0.00243)	0.0046 (0.0123)	0.00145 (0.00475)	1e-05 (8.16e-05)	9e-05 (0.000501)	0.00236 (0.00712)
del 17q11 2	132 (26%)	369	0.00035 (0.00158)	0.00015 (0.000755)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0052 (0.0137)	0.00672 (0.0172)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.126 (0.191)	0.00135 (0.0045)	0.256 (0.342)	0.0977 (0.156)
del xp11 3	149 (30%)	352	0.0794 (0.134)	0.401 (0.487)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0132 (0.0301)	0.0959 (0.154)	6e-05 (0.000349)	0.00217 (0.00665)	0.00015 (0.000755)	0.00059 (0.0024)	0.00072 (0.00273)	0.00095 (0.00337)
del xq22 3	114 (23%)	387	0.00687 (0.0174)	0.0106 (0.0251)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.778 (0.814)	0.613 (0.673)	0.00178 (0.00557)	0.334 (0.42)	1e-05 (8.16e-05)	0.00011 (0.000589)	0.00028 (0.00129)	0.0165 (0.0357)
amp 7p11 2	256 (51%)	245	0.0905 (0.148)	0.0299 (0.0586)	1e-05 (8.16e-05)	0.0221 (0.0458)	0.556 (0.625)	0.213 (0.293)	0.00055 (0.00225)	4e-05 (0.000247)	0.0162 (0.0353)	0.0467 (0.0861)	0.0247 (0.0502)	0.433 (0.515)
amp 9p13 3	136 (27%)	365	0.198 (0.275)	0.716 (0.762)	1e-05 (8.16e-05)	0.00794 (0.0196)	0.0115 (0.0267)	0.00012 (0.000636)	0.00179 (0.00557)	0.00119 (0.00405)	0.00044 (0.00191)	0.00374 (0.0104)	0.413 (0.495)	0.805 (0.837)
amp 15q26 3	179 (36%)	322	0.247 (0.332)	0.0509 (0.0927)	2e-05 (0.000142)	0.00079 (0.00295)	0.309 (0.396)	0.246 (0.332)	2e-05 (0.000142)	0.00258 (0.00767)	0.00179 (0.00557)	0.00637 (0.0164)	0.00083 (0.00306)	0.0103 (0.0244)
amp 18p11 32	179 (36%)	322	0.0537 (0.0971)	0.0046 (0.0123)	1e-05 (8.16e-05)	5e-05 (3e-04)	0.0888 (0.146)	0.104 (0.163)	0.0206 (0.0433)	0.00143 (0.0047)	0.00275 (0.00801)	0.0948 (0.154)	0.0331 (0.0646)	0.026 (0.0523)
del 4q35 2	331 (66%)	170	0.0904 (0.148)	0.205 (0.283)	1e-05 (8.16e-05)	0.00993 (0.0238)	0.112 (0.173)	0.1 (0.159)	2e-05 (0.000142)	0.00325 (0.00925)	2e-05 (0.000142)	0.0079 (0.0196)	0.00108 (0.00375)	0.0011 (0.0038)
del 5q31 1	386 (77%)	115	0.275 (0.361)	0.276 (0.362)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.275 (0.361)	0.526 (0.598)	0.00723 (0.0181)	0.00649 (0.0166)	0.0156 (0.0341)	3e-05 (0.000193)	0.00015 (0.000755)	0.0211 (0.0443)
del 6q26	135 (27%)	366	0.0597 (0.106)	0.00525 (0.0138)	0.0043 (0.0117)	0.00175 (0.0055)	0.36 (0.444)	0.942 (0.95)	0.00111 (0.00383)	0.00814 (0.02)	0.0278 (0.0553)	0.0748 (0.128)	0.00069 (0.00267)	0.0439 (0.0819)
del 10p15 3	228 (46%)	273	0.514 (0.589)	0.448 (0.527)	2e-05 (0.000142)	4e-05 (0.000247)	0.0679 (0.118)	0.285 (0.371)	1e-05 (8.16e-05)	0.00026 (0.00122)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	4e-05 (0.000247)	0.0447 (0.0832)
del 11p15 5	245 (49%)	256	0.00223 (0.00679)	0.0108 (0.0256)	1e-05 (8.16e-05)	0.00014 (0.000719)	0.0531 (0.0963)	0.00855 (0.0209)	0.00795 (0.0196)	0.0822 (0.137)	0.00071 (0.00271)	0.088 (0.145)	0.00288 (0.00834)	0.193 (0.269)
del 14q11 2	175 (35%)	326	0.00524 (0.0138)	0.0335 (0.0652)	6e-05 (0.000349)	0.0692 (0.119)	0.104 (0.163)	0.118 (0.18)	8e-05 (0.000453)	0.00015 (0.000755)	0.069 (0.119)	0.00995 (0.0238)	0.00325 (0.00925)	0.0024 (0.00722)
del xp21 1	151 (30%)	350	0.316 (0.404)	0.478 (0.558)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.274 (0.361)	0.308 (0.394)	5e-05 (3e-04)	0.00062 (0.00245)	0.00143 (0.0047)	0.00119 (0.00405)	0.00037 (0.00163)	0.00108 (0.00375)
amp 14q32 33	158 (32%)	343	0.108 (0.168)	0.0156 (0.0341)	1e-05 (8.16e-05)	9e-05 (0.000501)	0.0241 (0.0494)	0.144 (0.214)	0.00037 (0.00163)	0.00041 (0.00178)	0.457 (0.536)	0.43 (0.514)	0.00328 (0.00928)	0.549 (0.62)
amp 19q12	225 (45%)	276	0.502 (0.58)	0.648 (0.703)	1e-05 (8.16e-05)	0.0549 (0.0989)	0.0256 (0.0516)	0.845 (0.874)	0.00124 (0.0042)	0.0386 (0.0739)	0.0109 (0.0256)	0.565 (0.632)	0.00978 (0.0236)	0.0112 (0.0263)
del 10p15 1	211 (42%)	290	0.253 (0.34)	0.434 (0.515)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0817 (0.137)	0.404 (0.489)	1e-05 (8.16e-05)	7e-05 (0.000401)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.00037 (0.00163)	0.095 (0.154)
del 16q23 1	210 (42%)	291	0.987 (0.988)	0.114 (0.175)	0.0404 (0.0768)	0.205 (0.283)	0.007 (0.0177)	0.405 (0.489)	0.0456 (0.0843)	0.0376 (0.0723)	0.00463 (0.0124)	0.438 (0.519)	0.0131 (0.03)	0.0009 (0.00324)
del 22q13 32	127 (25%)	374	0.00047 (0.00198)	0.0105 (0.0248)	0.00013 (0.000681)	0.238 (0.322)	0.0433 (0.0811)	0.447 (0.526)	0.0001 (0.000544)	1e-05 (8.16e-05)	0.155 (0.226)	0.00055 (0.00225)	0.655 (0.71)	0.145 (0.215)
del xp22 2	155 (31%)	346	0.662 (0.716)	0.527 (0.599)	0.00014 (0.000719)	5e-05 (3e-04)	0.674 (0.726)	0.252 (0.338)	0.00461 (0.0123)	0.00982 (0.0236)	0.0246 (0.0502)	0.111 (0.172)	0.0003 (0.00138)	0.00598 (0.0155)
amp 20p12 2	280 (56%)	221	0.00143 (0.0047)	0.00235 (0.00711)	1e-05 (8.16e-05)	0.00274 (0.008)	0.147 (0.217)	0.551 (0.621)	0.00677 (0.0172)	0.0147 (0.033)	0.0821 (0.137)	0.648 (0.703)	0.0887 (0.146)	0.759 (0.798)
del 5q12 1	369 (74%)	132	0.349 (0.435)	0.433 (0.515)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.0631 (0.111)	0.434 (0.516)	0.00068 (0.00266)	0.00132 (0.00441)	0.139 (0.208)	6e-05 (0.000349)	0.00012 (0.000636)	0.0616 (0.109)
del 6p25 3	134 (27%)	367	0.541 (0.612)	0.281 (0.368)	7e-05 (0.000401)	3e-05 (0.000193)	0.942 (0.95)	0.478 (0.558)	1e-05 (8.16e-05)	1e-05 (8.16e-05)	0.039 (0.0744)	0.00086 (0.00314)	0.262 (0.347)	0.67 (0.722)
del 7q36 3	104 (21%)	397	0.302 (0.39)	0.0489 (0.0895)	0.00025 (0.00117)	0.0689 (0.119)	0.345 (0.432)	0.197 (0.274)	0.00018 (0.000892)	0.00127 (0.00427)	0.421 (0.505)	0.00442 (0.012)	0.175 (0.25)	0.00046 (0.00197)
del 9p21 3	388 (77%)	113	0.214 (0.295)	0.258 (0.343)	1e-05 (8.16e-05)	0.0958 (0.154)	0.635 (0.693)	0.275 (0.361)	0.00174 (0.0055)	0.0155 (0.0341)	0.352 (0.438)	0.0121 (0.0277)	0.00091 (0.00326)	0.0373 (0.0717)
del 17q25 3	102 (20%)	399	0.0275 (0.0548)	0.0113 (0.0264)	3e-05 (0.000193)	0.0826 (0.138)	0.776 (0.813)	0.574 (0.641)	0.00307 (0.00884)	0.00127 (0.00427)	0.405 (0.489)	0.0134 (0.0304)	0.0826 (0.138)	0.904 (0.924)
del 19p13 3	236 (47%)	265	0.39 (0.475)	0.234 (0.319)	1e-05 (8.16e-05)	0.102 (0.161)	0.152 (0.221)	0.116 (0.177)	0.0705 (0.121)	0.0219 (0.0455)	0.0273 (0.0547)	0.00086 (0.00314)	0.00384 (0.0107)	0.00426 (0.0116)
del 19q13 32	149 (30%)	352	0.79 (0.824)	0.589 (0.652)	1e-05 (8.16e-05)	0.0017 (0.00539)	0.0141 (0.0318)	0.442 (0.522)	0.018 (0.0385)	0.00713 (0.0179)	0.00435 (0.0118)	0.505 (0.582)	0.101 (0.159)	0.254 (0.34)
amp 6q12	152 (30%)	349	0.883 (0.907)	0.728 (0.77)	0.00016 (0.000801)	0.246 (0.332)	0.553 (0.622)	0.792 (0.825)	0.00095 (0.00337)	0.0055 (0.0143)	0.00315 (0.00904)	0.0229 (0.0472)	0.235 (0.319)	0.587 (0.651)
amp 19q13 2	234 (47%)	267	0.44 (0.521)	0.258 (0.343)	1e-05 (8.16e-05)	0.0931 (0.152)	0.0488 (0.0895)	0.518 (0.592)	0.00353 (0.00993)	0.0807 (0.136)	0.0363 (0.0699)	0.501 (0.58)	0.105 (0.164)	0.0137 (0.0311)
amp 22q11 21	256 (51%)	245	0.181 (0.256)	0.157 (0.228)	1e-05 (8.16e-05)	3e-05 (0.000193)	0.0639 (0.112)	0.641 (0.698)	6e-05 (0.000349)	0.00022 (0.00106)	0.38 (0.465)	0.0416 (0.0785)	0.0739 (0.127)	0.206 (0.283)
del 9p21 1	326 (65%)	175	0.329 (0.415)	0.285 (0.371)	1e-05 (8.16e-05)	0.0538 (0.0971)	0.348 (0.435)	0.506 (0.582)	0.00022 (0.00106)	0.00036 (0.00162)	0.0901 (0.148)	0.00918 (0.0224)	0.00138 (0.00458)	0.197 (0.274)
del 11q22 1	163 (33%)	338	0.483 (0.561)	0.177 (0.252)	0.00061 (0.00243)	0.00175 (0.0055)	0.279 (0.366)	0.277 (0.363)	0.0231 (0.0475)	0.0296 (0.0583)	0.162 (0.235)	0.0194 (0.041)	0.164 (0.236)	0.0955 (0.154)
del 21q11 2	244 (49%)	257	0.709 (0.755)	0.562 (0.629)	0.00089 (0.00321)	0.0181 (0.0387)	0.703 (0.751)	0.271 (0.358)	0.0624 (0.11)	0.436 (0.517)	3e-05 (0.000193)	4e-05 (0.000247)	0.00151 (0.00491)	0.0952 (0.154)
del 21q22 3	281 (56%)	220	0.896 (0.918)	0.128 (0.194)	2e-05 (0.000142)	0.00399 (0.011)	0.92 (0.935)	0.199 (0.276)	0.0651 (0.114)	0.0761 (0.13)	0.00055 (0.00225)	0.00047 (0.00198)	0.0273 (0.0547)	0.428 (0.511)
amp 5p15 33	387 (77%)	114	0.851 (0.88)	0.802 (0.834)	1e-05 (8.16e-05)	0.0001 (0.000544)	0.106 (0.166)	0.405 (0.489)	0.366 (0.45)	0.0656 (0.114)	0.0762 (0.13)	0.00544 (0.0142)	0.00348 (0.00982)	0.317 (0.404)
amp 12q15	178 (36%)	323	0.156 (0.227)	0.344 (0.432)	0.00041 (0.00178)	0.00538 (0.0141)	0.0741 (0.127)	0.368 (0.452)	0.00602 (0.0156)	0.0117 (0.0271)	0.128 (0.194)	0.643 (0.7)	0.153 (0.223)	0.136 (0.204)
amp 14q13 3	159 (32%)	342	0.41 (0.493)	0.0266 (0.0534)	1e-05 (8.16e-05)	0.409 (0.493)	0.259 (0.344)	0.356 (0.44)	0.0675 (0.117)	0.00261 (0.00774)	0.00405 (0.0111)	0.111 (0.172)	0.148 (0.217)	0.94 (0.95)
amp xq28	124 (25%)	377	0.913 (0.932)	0.87 (0.896)	0.00326 (0.00925)	0.00414 (0.0114)	0.413 (0.495)	0.863 (0.89)	0.0304 (0.0593)	0.308 (0.394)	0.0298 (0.0586)	0.164 (0.237)	0.558 (0.626)	0.303 (0.39)
del 2p25 3	50 (10%)	451	0.106 (0.166)	0.458 (0.536)	0.0119 (0.0274)	0.972 (0.977)	0.617 (0.678)	0.0418 (0.0788)	0.323 (0.41)	0.606 (0.668)	0.0113 (0.0264)	0.365 (0.45)	0.188 (0.264)	0.0282 (0.056)
del 8p23 2	341 (68%)	160	0.475 (0.555)	0.708 (0.755)	4e-05 (0.000247)	0.0249 (0.0506)	0.395 (0.481)	0.589 (0.652)	0.0846 (0.14)	0.0919 (0.15)	0.0152 (0.0338)	0.0656 (0.114)	0.12 (0.183)	0.0154 (0.0339)
del 16p13 3	187 (37%)	314	0.179 (0.253)	0.445 (0.524)	0.00021 (0.00103)	0.00979 (0.0236)	0.148 (0.217)	0.292 (0.378)	0.303 (0.391)	0.919 (0.935)	0.0179 (0.0384)	0.634 (0.693)	0.00232 (0.00704)	0.144 (0.215)
del 17p11 2	272 (54%)	229	0.205 (0.283)	0.113 (0.174)	1e-05 (8.16e-05)	0.0534 (0.0967)	0.576 (0.641)	0.0958 (0.154)	0.185 (0.261)	0.0161 (0.0349)	0.151 (0.22)	0.0256 (0.0517)	0.0134 (0.0304)	0.139 (0.207)
amp 6p12 1	166 (33%)	335	0.727 (0.769)	0.495 (0.574)	3e-05 (0.000193)	0.369 (0.453)	0.35 (0.435)	0.507 (0.583)	0.00092 (0.00328)	0.0641 (0.113)	0.0103 (0.0246)	0.118 (0.181)	0.451 (0.53)	0.1 (0.159)
amp 8p11 23	238 (48%)	263	0.0218 (0.0455)	0.0916 (0.15)	0.0601 (0.107)	0.0301 (0.0588)	0.326 (0.412)	0.229 (0.312)	0.0586 (0.105)	0.057 (0.102)	0.731 (0.771)	0.173 (0.248)	0.0215 (0.0449)	0.306 (0.393)
amp 20q11 21	306 (61%)	195	0.767 (0.804)	0.506 (0.582)	1e-05 (8.16e-05)	0.0119 (0.0274)	0.494 (0.573)	0.977 (0.979)	0.289 (0.375)	0.945 (0.953)	0.157 (0.227)	0.37 (0.453)	0.0149 (0.0332)	0.138 (0.207)
del 7q11 22	48 (10%)	453	0.839 (0.869)	0.698 (0.747)	0.00961 (0.0233)	0.73 (0.771)	0.215 (0.295)	0.576 (0.641)	0.00076 (0.00286)	0.00107 (0.00375)	0.401 (0.487)	0.375 (0.46)	0.726 (0.769)	0.32 (0.408)
del 11q25	184 (37%)	317	0.942 (0.95)	0.704 (0.752)	0.00011 (0.000589)	0.0169 (0.0364)	0.124 (0.189)	0.227 (0.31)	0.0352 (0.0681)	0.147 (0.217)	0.0952 (0.154)	0.148 (0.217)	0.218 (0.299)	0.151 (0.22)
del 13q12 11	331 (66%)	170	0.199 (0.276)	0.571 (0.638)	2e-05 (0.000142)	0.0409 (0.0776)	0.662 (0.716)	0.332 (0.419)	0.896 (0.918)	0.971 (0.977)	0.427 (0.511)	0.382 (0.466)	0.115 (0.177)	0.0123 (0.0281)
del 13q14 2	344 (69%)	157	0.123 (0.187)	0.0998 (0.159)	2e-05 (0.000142)	0.0254 (0.0515)	0.623 (0.683)	0.192 (0.269)	0.481 (0.56)	0.576 (0.641)	0.136 (0.205)	0.145 (0.216)	0.0147 (0.033)	0.0803 (0.136)
del 15q21 1	169 (34%)	332	0.511 (0.586)	0.762 (0.8)	2e-05 (0.000142)	0.0757 (0.129)	0.646 (0.703)	0.172 (0.247)	0.189 (0.266)	0.245 (0.331)	0.00128 (0.00429)	0.0975 (0.156)	0.0283 (0.056)	0.102 (0.161)
amp 4q12	119 (24%)	382	0.684 (0.735)	0.88 (0.904)	0.00256 (0.00766)	0.0989 (0.158)	0.905 (0.925)	0.0719 (0.124)	0.0506 (0.0923)	0.58 (0.644)	0.0815 (0.137)	0.35 (0.435)	0.196 (0.273)	0.0462 (0.0854)
amp 5p12	354 (71%)	147	0.938 (0.95)	0.759 (0.798)	1e-05 (8.16e-05)	0.0001 (0.000544)	0.19 (0.266)	0.81 (0.841)	0.356 (0.44)	0.9 (0.921)	0.596 (0.658)	0.0784 (0.133)	0.18 (0.255)	0.721 (0.766)
amp 8q24 21	352 (70%)	149	0.916 (0.934)	0.782 (0.817)	1e-05 (8.16e-05)	0.0165 (0.0357)	0.109 (0.169)	0.678 (0.728)	0.735 (0.775)	0.549 (0.62)	0.289 (0.375)	0.257 (0.343)	0.167 (0.241)	1 (1.00)
amp 13q34	91 (18%)	410	0.948 (0.954)	0.833 (0.863)	0.00268 (0.0079)	0.483 (0.561)	0.178 (0.252)	0.176 (0.251)	0.667 (0.72)	0.107 (0.166)	0.259 (0.344)	0.0336 (0.0652)	0.976 (0.979)	0.592 (0.654)
del 15q11 2	167 (33%)	334	0.635 (0.693)	0.523 (0.596)	1e-05 (8.16e-05)	0.522 (0.595)	0.346 (0.433)	0.181 (0.255)	0.14 (0.209)	0.0616 (0.109)	0.0171 (0.0368)	0.536 (0.607)	0.0966 (0.155)	0.261 (0.346)
del 18q23	234 (47%)	267	0.677 (0.728)	0.171 (0.246)	0.00154 (0.005)	0.132 (0.2)	0.618 (0.678)	0.318 (0.405)	0.935 (0.948)	0.484 (0.561)	0.284 (0.37)	0.538 (0.609)	0.00708 (0.0179)	0.52 (0.593)
del 22q11 21	95 (19%)	406	0.0868 (0.144)	0.0973 (0.156)	0.00776 (0.0193)	0.242 (0.328)	0.291 (0.376)	0.434 (0.515)	0.177 (0.252)	0.0002 (0.000981)	0.342 (0.43)	0.402 (0.488)	0.355 (0.44)	0.0836 (0.139)
del 3q11 1	79 (16%)	422	0.853 (0.88)	0.782 (0.817)	0.517 (0.591)	0.312 (0.399)	0.72 (0.766)	0.629 (0.688)	0.832 (0.863)	0.172 (0.247)	0.399 (0.485)	0.517 (0.591)	0.92 (0.935)	0.93 (0.945)
del 12q24 31	86 (17%)	415	0.667 (0.72)	0.598 (0.66)	0.566 (0.632)	0.692 (0.742)	0.866 (0.892)	0.151 (0.221)	0.723 (0.767)	0.695 (0.744)	0.0806 (0.136)	0.333 (0.419)	0.224 (0.307)	0.0873 (0.144)

'amp_1q21.2' versus 'MRNA_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.078

Table S1. Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 1(1Q21.2) MUTATED	18	36	17	16
AMP PEAK 1(1Q21.2) WILD-TYPE	23	14	17	13

Figure S1. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S2. Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 1(1Q21.2) MUTATED	21	43	11	29	120	34
AMP PEAK 1(1Q21.2) WILD-TYPE	22	72	18	58	49	24

Figure S2. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_1q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S3. Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 1(1Q21.2) MUTATED	40	55	43	46
AMP PEAK 1(1Q21.2) WILD-TYPE	50	40	14	79

Figure S3. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_1q21.2' versus 'RPPA_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.046

Table S4. Gene #1: 'amp_1q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 1(1Q21.2) MUTATED	51	55	56	9
AMP PEAK 1(1Q21.2) WILD-TYPE	54	54	30	17

Figure S4. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S5. Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 1(1Q21.2) MUTATED	41	104	83	29
AMP PEAK 1(1Q21.2) WILD-TYPE	65	46	76	54

Figure S5. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S6. Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 1(1Q21.2) MUTATED	63	123	71
AMP PEAK 1(1Q21.2) WILD-TYPE	115	66	60

Figure S6. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S7. Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 1(1Q21.2) MUTATED	109	38	43	54
AMP PEAK 1(1Q21.2) WILD-TYPE	75	49	81	26

Figure S7. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_1q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S8. Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 1(1Q21.2) MUTATED	64	67	89	24
AMP PEAK 1(1Q21.2) WILD-TYPE	25	51	110	45

Figure S8. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.0021

Table S9. Gene #1: 'amp_1q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 1(1Q21.2) MUTATED	23	65	22	56
AMP PEAK 1(1Q21.2) WILD-TYPE	38	50	44	36

Figure S9. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_1q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.026

Table S10. Gene #1: 'amp_1q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 1(1Q21.2) MUTATED	14	107	45
AMP PEAK 1(1Q21.2) WILD-TYPE	23	81	64

Figure S10. Get High-res Image Gene #1: 'amp_1q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2p16.1' versus 'MRNA_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0031

Table S11. Gene #2: 'amp_2p16.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 2(2P16.1) MUTATED	17	39	16	13
AMP PEAK 2(2P16.1) WILD-TYPE	24	11	18	16

Figure S11. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2p16.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.0017

Table S12. Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 2(2P16.1) MUTATED	24	42	19
AMP PEAK 2(2P16.1) WILD-TYPE	23	14	32

Figure S12. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2p16.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S13. Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 2(2P16.1) MUTATED	18	38	18	28	126	47
AMP PEAK 2(2P16.1) WILD-TYPE	25	77	11	59	43	11

Figure S13. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2p16.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S14. Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 2(2P16.1) MUTATED	40	71	41	52
AMP PEAK 2(2P16.1) WILD-TYPE	50	24	16	73

Figure S14. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2p16.1' versus 'RPPA_CNMF'

P value = 0.00797 (Fisher's exact test), Q value = 0.02

Table S15. Gene #2: 'amp_2p16.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 2(2P16.1) MUTATED	52	56	61	12
AMP PEAK 2(2P16.1) WILD-TYPE	53	53	25	14

Figure S15. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S16. Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 2(2P16.1) MUTATED	42	112	92	27
AMP PEAK 2(2P16.1) WILD-TYPE	64	38	67	56

Figure S16. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2p16.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S17. Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 2(2P16.1) MUTATED	82	131	60
AMP PEAK 2(2P16.1) WILD-TYPE	96	58	71

Figure S17. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S18. Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 2(2P16.1) MUTATED	107	61	47	48
AMP PEAK 2(2P16.1) WILD-TYPE	77	26	77	32

Figure S18. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2p16.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S19. Gene #2: 'amp_2p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 2(2P16.1) MUTATED	54	64	122	23
AMP PEAK 2(2P16.1) WILD-TYPE	35	54	77	46

Figure S19. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S20. Gene #2: 'amp_2p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 2(2P16.1) MUTATED	33	71	22	60
AMP PEAK 2(2P16.1) WILD-TYPE	28	44	44	32

Figure S20. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_2p16.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S21. Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 2(2P16.1) MUTATED	20	121	45
AMP PEAK 2(2P16.1) WILD-TYPE	17	67	64

Figure S21. Get High-res Image Gene #2: 'amp_2p16.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_2q31.2' versus 'MRNA_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.074

Table S22. Gene #3: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 3(2Q31.2) MUTATED	11	26	9	9
AMP PEAK 3(2Q31.2) WILD-TYPE	30	24	25	20

Figure S22. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_2q31.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 0.047

Table S23. Gene #3: 'amp_2q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 3(2Q31.2) MUTATED	13	28	14
AMP PEAK 3(2Q31.2) WILD-TYPE	34	28	37

Figure S23. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_2q31.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S24. Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 3(2Q31.2) MUTATED	9	20	8	22	86	27
AMP PEAK 3(2Q31.2) WILD-TYPE	34	95	21	65	83	31

Figure S24. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_2q31.2' versus 'METHLYATION_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0037

Table S25. Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 3(2Q31.2) MUTATED	26	47	25	33
AMP PEAK 3(2Q31.2) WILD-TYPE	64	48	32	92

Figure S25. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_2q31.2' versus 'RPPA_CNMF'

P value = 0.00928 (Fisher's exact test), Q value = 0.023

Table S26. Gene #3: 'amp_2q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 3(2Q31.2) MUTATED	28	36	43	9
AMP PEAK 3(2Q31.2) WILD-TYPE	77	73	43	17

Figure S26. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S27. Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 3(2Q31.2) MUTATED	26	77	50	18
AMP PEAK 3(2Q31.2) WILD-TYPE	80	73	109	65

Figure S27. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_2q31.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S28. Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 3(2Q31.2) MUTATED	42	91	38
AMP PEAK 3(2Q31.2) WILD-TYPE	136	98	93

Figure S28. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_2q31.2' versus 'MIRSEQ_CNMF'

P value = 0.00078 (Fisher's exact test), Q value = 0.0029

Table S29. Gene #3: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 3(2Q31.2) MUTATED	77	32	25	30
AMP PEAK 3(2Q31.2) WILD-TYPE	107	55	99	50

Figure S29. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_2q31.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00397 (Fisher's exact test), Q value = 0.011

Table S30. Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 3(2Q31.2) MUTATED	15	47	13	38
AMP PEAK 3(2Q31.2) WILD-TYPE	46	68	53	54

Figure S30. Get High-res Image Gene #3: 'amp_2q31.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MRNA_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0028

Table S31. Gene #4: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 4(3Q26.33) MUTATED	39	50	27	24
AMP PEAK 4(3Q26.33) WILD-TYPE	2	0	7	5

Figure S31. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0019

Table S32. Gene #4: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 4(3Q26.33) MUTATED	43	56	41
AMP PEAK 4(3Q26.33) WILD-TYPE	4	0	10

Figure S32. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S33. Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 4(3Q26.33) MUTATED	42	77	28	81	169	55
AMP PEAK 4(3Q26.33) WILD-TYPE	1	38	1	6	0	3

Figure S33. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S34. Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 4(3Q26.33) MUTATED	85	95	55	95
AMP PEAK 4(3Q26.33) WILD-TYPE	5	0	2	30

Figure S34. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.33' versus 'RPPA_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0027

Table S35. Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 4(3Q26.33) MUTATED	84	99	84	23
AMP PEAK 4(3Q26.33) WILD-TYPE	21	10	2	3

Figure S35. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_3q26.33' versus 'RPPA_CHIERARCHICAL'

P value = 0.00847 (Fisher's exact test), Q value = 0.021

Table S36. Gene #4: 'amp_3q26.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
AMP PEAK 4(3Q26.33) MUTATED	68	59	58	59	25	21
AMP PEAK 4(3Q26.33) WILD-TYPE	11	8	4	1	5	7

Figure S36. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S37. Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 4(3Q26.33) MUTATED	101	150	137	61
AMP PEAK 4(3Q26.33) WILD-TYPE	5	0	22	22

Figure S37. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S38. Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 4(3Q26.33) MUTATED	163	188	98
AMP PEAK 4(3Q26.33) WILD-TYPE	15	1	33

Figure S38. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S39. Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 4(3Q26.33) MUTATED	172	85	95	77
AMP PEAK 4(3Q26.33) WILD-TYPE	12	2	29	3

Figure S39. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S40. Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 4(3Q26.33) MUTATED	89	108	189	43
AMP PEAK 4(3Q26.33) WILD-TYPE	0	10	10	26

Figure S40. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S41. Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 4(3Q26.33) MUTATED	56	109	47	88
AMP PEAK 4(3Q26.33) WILD-TYPE	5	6	19	4

Figure S41. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S42. Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 4(3Q26.33) MUTATED	34	179	87
AMP PEAK 4(3Q26.33) WILD-TYPE	3	9	22

Figure S42. Get High-res Image Gene #4: 'amp_3q26.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q12' versus 'CN_CNMF'

P value = 0.00256 (Fisher's exact test), Q value = 0.0077

Table S43. Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 5(4Q12) MUTATED	12	15	10	16	44	22
AMP PEAK 5(4Q12) WILD-TYPE	31	100	19	71	125	36

Figure S43. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_4q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0462 (Fisher's exact test), Q value = 0.085

Table S44. Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 5(4Q12) MUTATED	13	41	17
AMP PEAK 5(4Q12) WILD-TYPE	24	147	92

Figure S44. Get High-res Image Gene #5: 'amp_4q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S45. Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 6(5P15.33) MUTATED	37	76	26	67	123	58
AMP PEAK 6(5P15.33) WILD-TYPE	6	39	3	20	46	0

Figure S45. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S46. Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 6(5P15.33) MUTATED	84	71	40	88
AMP PEAK 6(5P15.33) WILD-TYPE	6	24	17	37

Figure S46. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00544 (Fisher's exact test), Q value = 0.014

Table S47. Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 6(5P15.33) MUTATED	66	88	168	45
AMP PEAK 6(5P15.33) WILD-TYPE	23	30	31	24

Figure S47. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00348 (Fisher's exact test), Q value = 0.0098

Table S48. Gene #6: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 6(5P15.33) MUTATED	54	93	41	70
AMP PEAK 6(5P15.33) WILD-TYPE	7	22	25	22

Figure S48. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S49. Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 7(5P12) MUTATED	32	63	26	56	120	57
AMP PEAK 7(5P12) WILD-TYPE	11	52	3	31	49	1

Figure S49. Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p12' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S50. Gene #7: 'amp_5p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 7(5P12) MUTATED	78	67	37	75
AMP PEAK 7(5P12) WILD-TYPE	12	28	20	50

Figure S50. Get High-res Image Gene #7: 'amp_5p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p12.1' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S51. Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 8(6P12.1) MUTATED	15	23	8	20	71	29
AMP PEAK 8(6P12.1) WILD-TYPE	28	92	21	67	98	29

Figure S51. Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p12.1' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0033

Table S52. Gene #8: 'amp_6p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 8(6P12.1) MUTATED	19	60	59	26
AMP PEAK 8(6P12.1) WILD-TYPE	87	90	100	57

Figure S52. Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p12.1' versus 'MIRSEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.025

Table S53. Gene #8: 'amp_6p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 8(6P12.1) MUTATED	72	28	27	30
AMP PEAK 8(6P12.1) WILD-TYPE	112	59	97	50

Figure S53. Get High-res Image Gene #8: 'amp_6p12.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q12' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 8e-04

Table S54. Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 9(6Q12) MUTATED	10	19	7	24	66	26
AMP PEAK 9(6Q12) WILD-TYPE	33	96	22	63	103	32

Figure S54. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q12' versus 'MRNASEQ_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0034

Table S55. Gene #9: 'amp_6q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 9(6Q12) MUTATED	17	56	55	22
AMP PEAK 9(6Q12) WILD-TYPE	89	94	104	61

Figure S55. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0055 (Fisher's exact test), Q value = 0.014

Table S56. Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 9(6Q12) MUTATED	38	66	46
AMP PEAK 9(6Q12) WILD-TYPE	140	123	85

Figure S56. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q12' versus 'MIRSEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.009

Table S57. Gene #9: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 9(6Q12) MUTATED	70	22	25	29
AMP PEAK 9(6Q12) WILD-TYPE	114	65	99	51

Figure S57. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.047

Table S58. Gene #9: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 9(6Q12) MUTATED	36	30	66	14
AMP PEAK 9(6Q12) WILD-TYPE	53	88	133	55

Figure S58. Get High-res Image Gene #9: 'amp_6q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.059

Table S59. Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 10(7P11.2) MUTATED	23	37	21
AMP PEAK 10(7P11.2) WILD-TYPE	24	19	30

Figure S59. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S60. Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 10(7P11.2) MUTATED	33	44	16	22	107	34
AMP PEAK 10(7P11.2) WILD-TYPE	10	71	13	65	62	24

Figure S60. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7p11.2' versus 'METHLYATION_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.046

Table S61. Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 10(7P11.2) MUTATED	43	61	26	56
AMP PEAK 10(7P11.2) WILD-TYPE	47	34	31	69

Figure S61. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S62. Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 10(7P11.2) MUTATED	51	96	76	31
AMP PEAK 10(7P11.2) WILD-TYPE	55	54	83	52

Figure S62. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S63. Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 10(7P11.2) MUTATED	78	122	54
AMP PEAK 10(7P11.2) WILD-TYPE	100	67	77

Figure S63. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.035

Table S64. Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 10(7P11.2) MUTATED	99	53	50	45
AMP PEAK 10(7P11.2) WILD-TYPE	85	34	74	35

Figure S64. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.086

Table S65. Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 10(7P11.2) MUTATED	58	56	100	33
AMP PEAK 10(7P11.2) WILD-TYPE	31	62	99	36

Figure S65. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.05

Table S66. Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 10(7P11.2) MUTATED	29	60	25	57
AMP PEAK 10(7P11.2) WILD-TYPE	32	55	41	35

Figure S66. Get High-res Image Gene #10: 'amp_7p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S67. Gene #11: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 11(7Q21.2) MUTATED	30	39	22
AMP PEAK 11(7Q21.2) WILD-TYPE	17	17	29

Figure S67. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_7q21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S68. Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 11(7Q21.2) MUTATED	35	34	17	17	119	42
AMP PEAK 11(7Q21.2) WILD-TYPE	8	81	12	70	50	16

Figure S68. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_7q21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S69. Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 11(7Q21.2) MUTATED	43	67	31	45
AMP PEAK 11(7Q21.2) WILD-TYPE	47	28	26	80

Figure S69. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S70. Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 11(7Q21.2) MUTATED	49	107	74	32
AMP PEAK 11(7Q21.2) WILD-TYPE	57	43	85	51

Figure S70. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_7q21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S71. Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 11(7Q21.2) MUTATED	74	130	58
AMP PEAK 11(7Q21.2) WILD-TYPE	104	59	73

Figure S71. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S72. Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 11(7Q21.2) MUTATED	111	48	41	54
AMP PEAK 11(7Q21.2) WILD-TYPE	73	39	83	26

Figure S72. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_7q21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00098 (Fisher's exact test), Q value = 0.0035

Table S73. Gene #11: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 11(7Q21.2) MUTATED	63	63	100	28
AMP PEAK 11(7Q21.2) WILD-TYPE	26	55	99	41

Figure S73. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0079

Table S74. Gene #11: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 11(7Q21.2) MUTATED	26	61	23	58
AMP PEAK 11(7Q21.2) WILD-TYPE	35	54	43	34

Figure S74. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_7q21.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0419 (Fisher's exact test), Q value = 0.079

Table S75. Gene #11: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 11(7Q21.2) MUTATED	15	106	47
AMP PEAK 11(7Q21.2) WILD-TYPE	22	82	62

Figure S75. Get High-res Image Gene #11: 'amp_7q21.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 0.0218 (Fisher's exact test), Q value = 0.045

Table S76. Gene #12: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 12(8P11.23) MUTATED	29	23	13	13
AMP PEAK 12(8P11.23) WILD-TYPE	12	27	21	16

Figure S76. Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.059

Table S77. Gene #12: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 12(8P11.23) MUTATED	46	53	21	49
AMP PEAK 12(8P11.23) WILD-TYPE	44	42	36	76

Figure S77. Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.045

Table S78. Gene #12: 'amp_8p11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 12(8P11.23) MUTATED	28	50	21	52
AMP PEAK 12(8P11.23) WILD-TYPE	33	65	45	40

Figure S78. Get High-res Image Gene #12: 'amp_8p11.23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S79. Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 13(8Q24.21) MUTATED	39	69	24	52	115	53
AMP PEAK 13(8Q24.21) WILD-TYPE	4	46	5	35	54	5

Figure S79. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.036

Table S80. Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 13(8Q24.21) MUTATED	71	74	36	79
AMP PEAK 13(8Q24.21) WILD-TYPE	19	21	21	46

Figure S80. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S81. Gene #14: 'amp_9p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 14(9P13.3) MUTATED	16	20	8	10	66	16
AMP PEAK 14(9P13.3) WILD-TYPE	27	95	21	77	103	42

Figure S81. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_9p13.3' versus 'METHLYATION_CNMF'

P value = 0.00794 (Fisher's exact test), Q value = 0.02

Table S82. Gene #14: 'amp_9p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 14(9P13.3) MUTATED	25	38	18	24
AMP PEAK 14(9P13.3) WILD-TYPE	65	57	39	101

Figure S82. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_9p13.3' versus 'RPPA_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.027

Table S83. Gene #14: 'amp_9p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 14(9P13.3) MUTATED	23	23	35	6
AMP PEAK 14(9P13.3) WILD-TYPE	82	86	51	20

Figure S83. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_9p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S84. Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
AMP PEAK 14(9P13.3) MUTATED	29	16	17	22	0	3
AMP PEAK 14(9P13.3) WILD-TYPE	50	51	45	38	30	25

Figure S84. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_9p13.3' versus 'MRNASEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0056

Table S85. Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 14(9P13.3) MUTATED	21	57	43	15
AMP PEAK 14(9P13.3) WILD-TYPE	85	93	116	68

Figure S85. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_9p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.004

Table S86. Gene #14: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 14(9P13.3) MUTATED	34	68	34
AMP PEAK 14(9P13.3) WILD-TYPE	144	121	97

Figure S86. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_9p13.3' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0019

Table S87. Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 14(9P13.3) MUTATED	59	23	18	31
AMP PEAK 14(9P13.3) WILD-TYPE	125	64	106	49

Figure S87. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_9p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00374 (Fisher's exact test), Q value = 0.01

Table S88. Gene #14: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 14(9P13.3) MUTATED	32	41	48	10
AMP PEAK 14(9P13.3) WILD-TYPE	57	77	151	59

Figure S88. Get High-res Image Gene #14: 'amp_9p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.078

Table S89. Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 15(11Q13.3) MUTATED	17	10	12	14
AMP PEAK 15(11Q13.3) WILD-TYPE	24	40	22	15

Figure S89. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.066

Table S90. Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 15(11Q13.3) MUTATED	19	12	22
AMP PEAK 15(11Q13.3) WILD-TYPE	28	44	29

Figure S90. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0053

Table S91. Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 15(11Q13.3) MUTATED	26	30	14	35	56	24
AMP PEAK 15(11Q13.3) WILD-TYPE	17	85	15	52	113	34

Figure S91. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00085

Table S92. Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 15(11Q13.3) MUTATED	50	37	20	32
AMP PEAK 15(11Q13.3) WILD-TYPE	40	58	37	93

Figure S92. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 0.0211 (Fisher's exact test), Q value = 0.044

Table S93. Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 15(11Q13.3) MUTATED	44	42	70	29
AMP PEAK 15(11Q13.3) WILD-TYPE	62	108	89	54

Figure S93. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.034

Table S94. Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 15(11Q13.3) MUTATED	78	39	41	20
AMP PEAK 15(11Q13.3) WILD-TYPE	106	48	83	60

Figure S94. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00465 (Fisher's exact test), Q value = 0.012

Table S95. Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 15(11Q13.3) MUTATED	24	47	89	18
AMP PEAK 15(11Q13.3) WILD-TYPE	65	71	110	51

Figure S95. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0053

Table S96. Gene #15: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 15(11Q13.3) MUTATED	25	57	14	32
AMP PEAK 15(11Q13.3) WILD-TYPE	36	58	52	60

Figure S96. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.041

Table S97. Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 15(11Q13.3) MUTATED	20	76	32
AMP PEAK 15(11Q13.3) WILD-TYPE	17	112	77

Figure S97. Get High-res Image Gene #15: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 0.00197 (Fisher's exact test), Q value = 0.0061

Table S98. Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 16(12P13.33) MUTATED	11	33	14	13
AMP PEAK 16(12P13.33) WILD-TYPE	30	17	20	16

Figure S98. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 0.045

Table S99. Gene #16: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 16(12P13.33) MUTATED	17	34	20
AMP PEAK 16(12P13.33) WILD-TYPE	30	22	31

Figure S99. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S100. Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 16(12P13.33) MUTATED	24	40	12	32	108	39
AMP PEAK 16(12P13.33) WILD-TYPE	19	75	17	55	61	19

Figure S100. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 0.00371 (Fisher's exact test), Q value = 0.01

Table S101. Gene #16: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 16(12P13.33) MUTATED	51	58	38	52
AMP PEAK 16(12P13.33) WILD-TYPE	39	37	19	73

Figure S101. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S102. Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 16(12P13.33) MUTATED	35	98	92	28
AMP PEAK 16(12P13.33) WILD-TYPE	71	52	67	55

Figure S102. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.0059

Table S103. Gene #16: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 16(12P13.33) MUTATED	72	111	70
AMP PEAK 16(12P13.33) WILD-TYPE	106	78	61

Figure S103. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.032

Table S104. Gene #16: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 16(12P13.33) MUTATED	104	48	49	46
AMP PEAK 16(12P13.33) WILD-TYPE	80	39	75	34

Figure S104. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00267 (Fisher's exact test), Q value = 0.0079

Table S105. Gene #16: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 16(12P13.33) MUTATED	57	58	108	24
AMP PEAK 16(12P13.33) WILD-TYPE	32	60	91	45

Figure S105. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.0085

Table S106. Gene #16: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 16(12P13.33) MUTATED	34	69	22	54
AMP PEAK 16(12P13.33) WILD-TYPE	27	46	44	38

Figure S106. Get High-res Image Gene #16: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12q15' versus 'CN_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S107. Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 17(12Q15) MUTATED	16	30	8	20	80	24
AMP PEAK 17(12Q15) WILD-TYPE	27	85	21	67	89	34

Figure S107. Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00538 (Fisher's exact test), Q value = 0.014

Table S108. Gene #17: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 17(12Q15) MUTATED	29	45	24	32
AMP PEAK 17(12Q15) WILD-TYPE	61	50	33	93

Figure S108. Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 0.00602 (Fisher's exact test), Q value = 0.016

Table S109. Gene #17: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 17(12Q15) MUTATED	27	69	54	26
AMP PEAK 17(12Q15) WILD-TYPE	79	81	105	57

Figure S109. Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.027

Table S110. Gene #17: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 17(12Q15) MUTATED	48	73	55
AMP PEAK 17(12Q15) WILD-TYPE	130	116	76

Figure S110. Get High-res Image Gene #17: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0079

Table S111. Gene #18: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 18(13Q34) MUTATED	10	14	11	8	33	15
AMP PEAK 18(13Q34) WILD-TYPE	33	101	18	79	136	43

Figure S111. Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0336 (Fisher's exact test), Q value = 0.065

Table S112. Gene #18: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 18(13Q34) MUTATED	8	27	41	10
AMP PEAK 18(13Q34) WILD-TYPE	81	91	158	59

Figure S112. Get High-res Image Gene #18: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.053

Table S113. Gene #19: 'amp_14q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 19(14Q13.3) MUTATED	23	15	13
AMP PEAK 19(14Q13.3) WILD-TYPE	24	41	38

Figure S113. Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S114. Gene #19: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 19(14Q13.3) MUTATED	35	33	12	14	50	15
AMP PEAK 19(14Q13.3) WILD-TYPE	8	82	17	73	119	43

Figure S114. Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00261 (Fisher's exact test), Q value = 0.0077

Table S115. Gene #19: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 19(14Q13.3) MUTATED	73	56	30
AMP PEAK 19(14Q13.3) WILD-TYPE	105	133	101

Figure S115. Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00405 (Fisher's exact test), Q value = 0.011

Table S116. Gene #19: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 19(14Q13.3) MUTATED	75	26	38	15
AMP PEAK 19(14Q13.3) WILD-TYPE	109	61	86	65

Figure S116. Get High-res Image Gene #19: 'amp_14q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q32.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.034

Table S117. Gene #20: 'amp_14q32.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 20(14Q32.33) MUTATED	22	17	10
AMP PEAK 20(14Q32.33) WILD-TYPE	25	39	41

Figure S117. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q32.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S118. Gene #20: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 20(14Q32.33) MUTATED	33	28	13	11	59	14
AMP PEAK 20(14Q32.33) WILD-TYPE	10	87	16	76	110	44

Figure S118. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q32.33' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S119. Gene #20: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 20(14Q32.33) MUTATED	32	47	13	27
AMP PEAK 20(14Q32.33) WILD-TYPE	58	48	44	98

Figure S119. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q32.33' versus 'RPPA_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.049

Table S120. Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 20(14Q32.33) MUTATED	25	44	25	12
AMP PEAK 20(14Q32.33) WILD-TYPE	80	65	61	14

Figure S120. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S121. Gene #20: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 20(14Q32.33) MUTATED	45	58	38	17
AMP PEAK 20(14Q32.33) WILD-TYPE	61	92	121	66

Figure S121. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q32.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.0018

Table S122. Gene #20: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 20(14Q32.33) MUTATED	66	68	24
AMP PEAK 20(14Q32.33) WILD-TYPE	112	121	107

Figure S122. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q32.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0093

Table S123. Gene #20: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 20(14Q32.33) MUTATED	22	35	10	38
AMP PEAK 20(14Q32.33) WILD-TYPE	39	80	56	54

Figure S123. Get High-res Image Gene #20: 'amp_14q32.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S124. Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 21(15Q26.3) MUTATED	8	23	15	32	83	18
AMP PEAK 21(15Q26.3) WILD-TYPE	35	92	14	55	86	40

Figure S124. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0029

Table S125. Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 21(15Q26.3) MUTATED	33	43	25	27
AMP PEAK 21(15Q26.3) WILD-TYPE	57	52	32	98

Figure S125. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S126. Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 21(15Q26.3) MUTATED	24	76	52	24
AMP PEAK 21(15Q26.3) WILD-TYPE	82	74	107	59

Figure S126. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00258 (Fisher's exact test), Q value = 0.0077

Table S127. Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 21(15Q26.3) MUTATED	57	84	35
AMP PEAK 21(15Q26.3) WILD-TYPE	121	105	96

Figure S127. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 0.00179 (Fisher's exact test), Q value = 0.0056

Table S128. Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 21(15Q26.3) MUTATED	65	37	31	40
AMP PEAK 21(15Q26.3) WILD-TYPE	119	50	93	40

Figure S128. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00637 (Fisher's exact test), Q value = 0.016

Table S129. Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 21(15Q26.3) MUTATED	44	39	74	16
AMP PEAK 21(15Q26.3) WILD-TYPE	45	79	125	53

Figure S129. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0031

Table S130. Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 21(15Q26.3) MUTATED	15	47	12	41
AMP PEAK 21(15Q26.3) WILD-TYPE	46	68	54	51

Figure S130. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.024

Table S131. Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 21(15Q26.3) MUTATED	12	77	26
AMP PEAK 21(15Q26.3) WILD-TYPE	25	111	83

Figure S131. Get High-res Image Gene #21: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q25.1' versus 'MRNA_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.011

Table S132. Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 22(17Q25.1) MUTATED	18	31	10	20
AMP PEAK 22(17Q25.1) WILD-TYPE	23	19	24	9

Figure S132. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S133. Gene #22: 'amp_17q25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 22(17Q25.1) MUTATED	22	27	8	33	113	33
AMP PEAK 22(17Q25.1) WILD-TYPE	21	88	21	54	56	25

Figure S133. Get High-res Image Gene #22: '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 = 8.2e-05

Table S134. Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 22(17Q25.1) MUTATED	41	61	28	37
AMP PEAK 22(17Q25.1) WILD-TYPE	49	34	29	88

Figure S134. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q25.1' versus 'RPPA_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0022

Table S135. Gene #22: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 22(17Q25.1) MUTATED	41	47	56	8
AMP PEAK 22(17Q25.1) WILD-TYPE	64	62	30	18

Figure S135. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S136. Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 22(17Q25.1) MUTATED	40	95	71	28
AMP PEAK 22(17Q25.1) WILD-TYPE	66	55	88	55

Figure S136. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S137. Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 22(17Q25.1) MUTATED	67	115	52
AMP PEAK 22(17Q25.1) WILD-TYPE	111	74	79

Figure S137. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.0025

Table S138. Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 22(17Q25.1) MUTATED	99	45	39	40
AMP PEAK 22(17Q25.1) WILD-TYPE	85	42	85	40

Figure S138. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00473 (Fisher's exact test), Q value = 0.013

Table S139. Gene #22: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 22(17Q25.1) MUTATED	53	51	97	22
AMP PEAK 22(17Q25.1) WILD-TYPE	36	67	102	47

Figure S139. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00065 (Fisher's exact test), Q value = 0.0025

Table S140. Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 22(17Q25.1) MUTATED	25	62	17	50
AMP PEAK 22(17Q25.1) WILD-TYPE	36	53	49	42

Figure S140. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.051

Table S141. Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 22(17Q25.1) MUTATED	14	99	41
AMP PEAK 22(17Q25.1) WILD-TYPE	23	89	68

Figure S141. Get High-res Image Gene #22: 'amp_17q25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18p11.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S142. Gene #23: 'amp_18p11.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 23(18P11.32) MUTATED	13	30	13
AMP PEAK 23(18P11.32) WILD-TYPE	34	26	38

Figure S142. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18p11.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S143. Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 23(18P11.32) MUTATED	19	23	10	20	86	21
AMP PEAK 23(18P11.32) WILD-TYPE	24	92	19	67	83	37

Figure S143. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_18p11.32' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S144. Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 23(18P11.32) MUTATED	39	48	19	26
AMP PEAK 23(18P11.32) WILD-TYPE	51	47	38	99

Figure S144. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.043

Table S145. Gene #23: 'amp_18p11.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 23(18P11.32) MUTATED	34	68	54	22
AMP PEAK 23(18P11.32) WILD-TYPE	72	82	105	61

Figure S145. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18p11.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0047

Table S146. Gene #23: 'amp_18p11.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 23(18P11.32) MUTATED	50	86	42
AMP PEAK 23(18P11.32) WILD-TYPE	128	103	89

Figure S146. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18p11.32' versus 'MIRSEQ_CNMF'

P value = 0.00275 (Fisher's exact test), Q value = 0.008

Table S147. Gene #23: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 23(18P11.32) MUTATED	72	38	28	33
AMP PEAK 23(18P11.32) WILD-TYPE	112	49	96	47

Figure S147. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0331 (Fisher's exact test), Q value = 0.065

Table S148. Gene #23: 'amp_18p11.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 23(18P11.32) MUTATED	18	46	15	39
AMP PEAK 23(18P11.32) WILD-TYPE	43	69	51	53

Figure S148. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_18p11.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.052

Table S149. Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 23(18P11.32) MUTATED	9	78	31
AMP PEAK 23(18P11.32) WILD-TYPE	28	110	78

Figure S149. Get High-res Image Gene #23: 'amp_18p11.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_18q11.2' versus 'MRNA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0027

Table S150. Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 24(18Q11.2) MUTATED	9	24	5	15
AMP PEAK 24(18Q11.2) WILD-TYPE	32	26	29	14

Figure S150. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_18q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.034

Table S151. Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 24(18Q11.2) MUTATED	10	27	16
AMP PEAK 24(18Q11.2) WILD-TYPE	37	29	35

Figure S151. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_18q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S152. Gene #24: 'amp_18q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 24(18Q11.2) MUTATED	16	15	7	16	78	19
AMP PEAK 24(18Q11.2) WILD-TYPE	27	100	22	71	91	39

Figure S152. Get High-res Image Gene #24: '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 = 8.2e-05

Table S153. Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 24(18Q11.2) MUTATED	24	49	16	18
AMP PEAK 24(18Q11.2) WILD-TYPE	66	46	41	107

Figure S153. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_18q11.2' versus 'RPPA_CNMF'

P value = 0.0191 (Fisher's exact test), Q value = 0.041

Table S154. Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 24(18Q11.2) MUTATED	31	26	37	5
AMP PEAK 24(18Q11.2) WILD-TYPE	74	83	49	21

Figure S154. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S155. Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 24(18Q11.2) MUTATED	25	64	52	9
AMP PEAK 24(18Q11.2) WILD-TYPE	81	86	107	74

Figure S155. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_18q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00045

Table S156. Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 24(18Q11.2) MUTATED	35	77	38
AMP PEAK 24(18Q11.2) WILD-TYPE	143	112	93

Figure S156. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_18q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0022 (Fisher's exact test), Q value = 0.0067

Table S157. Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 24(18Q11.2) MUTATED	64	26	22	31
AMP PEAK 24(18Q11.2) WILD-TYPE	120	61	102	49

Figure S157. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_18q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.0082

Table S158. Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 24(18Q11.2) MUTATED	38	32	62	11
AMP PEAK 24(18Q11.2) WILD-TYPE	51	86	137	58

Figure S158. Get High-res Image Gene #24: 'amp_18q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S159. Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 25(19Q12) MUTATED	19	40	9	19	100	38
AMP PEAK 25(19Q12) WILD-TYPE	24	75	20	68	69	20

Figure S159. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 0.0256 (Fisher's exact test), Q value = 0.052

Table S160. Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 25(19Q12) MUTATED	46	44	52	10
AMP PEAK 25(19Q12) WILD-TYPE	59	65	34	16

Figure S160. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.0042

Table S161. Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 25(19Q12) MUTATED	34	82	76	31
AMP PEAK 25(19Q12) WILD-TYPE	72	68	83	52

Figure S161. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.074

Table S162. Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 25(19Q12) MUTATED	67	96	60
AMP PEAK 25(19Q12) WILD-TYPE	111	93	71

Figure S162. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 0.0109 (Fisher's exact test), Q value = 0.026

Table S163. Gene #25: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 25(19Q12) MUTATED	93	45	41	38
AMP PEAK 25(19Q12) WILD-TYPE	91	42	83	42

Figure S163. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00978 (Fisher's exact test), Q value = 0.024

Table S164. Gene #25: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 25(19Q12) MUTATED	29	53	19	51
AMP PEAK 25(19Q12) WILD-TYPE	32	62	47	41

Figure S164. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.026

Table S165. Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 25(19Q12) MUTATED	18	97	37
AMP PEAK 25(19Q12) WILD-TYPE	19	91	72

Figure S165. Get High-res Image Gene #25: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S166. Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 26(19Q13.2) MUTATED	21	41	10	20	100	42
AMP PEAK 26(19Q13.2) WILD-TYPE	22	74	19	67	69	16

Figure S166. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.2' versus 'RPPA_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.089

Table S167. Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
AMP PEAK 26(19Q13.2) MUTATED	50	44	51	10
AMP PEAK 26(19Q13.2) WILD-TYPE	55	65	35	16

Figure S167. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.2' versus 'MRNASEQ_CNMF'

P value = 0.00353 (Fisher's exact test), Q value = 0.0099

Table S168. Gene #26: 'amp_19q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 26(19Q13.2) MUTATED	37	85	76	33
AMP PEAK 26(19Q13.2) WILD-TYPE	69	65	83	50

Figure S168. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.07

Table S169. Gene #26: 'amp_19q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 26(19Q13.2) MUTATED	91	48	46	42
AMP PEAK 26(19Q13.2) WILD-TYPE	93	39	78	38

Figure S169. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.031

Table S170. Gene #26: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
AMP PEAK 26(19Q13.2) MUTATED	19	100	39
AMP PEAK 26(19Q13.2) WILD-TYPE	18	88	70

Figure S170. Get High-res Image Gene #26: 'amp_19q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_20p12.2' versus 'MRNA_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0047

Table S171. Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
AMP PEAK 27(20P12.2) MUTATED	24	35	10	12
AMP PEAK 27(20P12.2) WILD-TYPE	17	15	24	17

Figure S171. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20p12.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00235 (Fisher's exact test), Q value = 0.0071

Table S172. Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
AMP PEAK 27(20P12.2) MUTATED	27	37	17
AMP PEAK 27(20P12.2) WILD-TYPE	20	19	34

Figure S172. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20p12.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S173. Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 27(20P12.2) MUTATED	32	45	21	25	118	39
AMP PEAK 27(20P12.2) WILD-TYPE	11	70	8	62	51	19

Figure S173. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20p12.2' versus 'METHLYATION_CNMF'

P value = 0.00274 (Fisher's exact test), Q value = 0.008

Table S174. Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 27(20P12.2) MUTATED	50	66	37	57
AMP PEAK 27(20P12.2) WILD-TYPE	40	29	20	68

Figure S174. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CNMF'

P value = 0.00677 (Fisher's exact test), Q value = 0.017

Table S175. Gene #27: 'amp_20p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 27(20P12.2) MUTATED	52	101	86	40
AMP PEAK 27(20P12.2) WILD-TYPE	54	49	73	43

Figure S175. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20p12.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0147 (Fisher's exact test), Q value = 0.033

Table S176. Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 27(20P12.2) MUTATED	94	121	64
AMP PEAK 27(20P12.2) WILD-TYPE	84	68	67

Figure S176. Get High-res Image Gene #27: 'amp_20p12.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S177. Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 28(20Q11.21) MUTATED	40	56	24	27	113	46
AMP PEAK 28(20Q11.21) WILD-TYPE	3	59	5	60	56	12

Figure S177. Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q11.21' versus 'METHLYATION_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.027

Table S178. Gene #28: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 28(20Q11.21) MUTATED	56	65	41	63
AMP PEAK 28(20Q11.21) WILD-TYPE	34	30	16	62

Figure S178. Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.033

Table S179. Gene #28: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
AMP PEAK 28(20Q11.21) MUTATED	39	72	30	65
AMP PEAK 28(20Q11.21) WILD-TYPE	22	43	36	27

Figure S179. Get High-res Image Gene #28: 'amp_20q11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S180. Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 29(22Q11.21) MUTATED	23	40	28	21	105	39
AMP PEAK 29(22Q11.21) WILD-TYPE	20	75	1	66	64	19

Figure S180. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_22q11.21' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S181. Gene #29: 'amp_22q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 29(22Q11.21) MUTATED	49	66	32	45
AMP PEAK 29(22Q11.21) WILD-TYPE	41	29	25	80

Figure S181. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S182. Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 29(22Q11.21) MUTATED	50	100	72	32
AMP PEAK 29(22Q11.21) WILD-TYPE	56	50	87	51

Figure S182. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S183. Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
AMP PEAK 29(22Q11.21) MUTATED	97	110	47
AMP PEAK 29(22Q11.21) WILD-TYPE	81	79	84

Figure S183. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_22q11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.078

Table S184. Gene #29: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
AMP PEAK 29(22Q11.21) MUTATED	48	55	114	27
AMP PEAK 29(22Q11.21) WILD-TYPE	41	63	85	42

Figure S184. Get High-res Image Gene #29: 'amp_22q11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_xq28' versus 'CN_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0093

Table S185. Gene #30: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
AMP PEAK 30(XQ28) MUTATED	12	22	5	12	50	23
AMP PEAK 30(XQ28) WILD-TYPE	31	93	24	75	119	35

Figure S185. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #3: 'CN_CNMF'

'amp_xq28' versus 'METHLYATION_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.011

Table S186. Gene #30: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
AMP PEAK 30(XQ28) MUTATED	22	36	10	22
AMP PEAK 30(XQ28) WILD-TYPE	68	59	47	103

Figure S186. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_xq28' versus 'MRNASEQ_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.059

Table S187. Gene #30: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
AMP PEAK 30(XQ28) MUTATED	17	48	37	19
AMP PEAK 30(XQ28) WILD-TYPE	89	102	122	64

Figure S187. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_xq28' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.059

Table S188. Gene #30: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
AMP PEAK 30(XQ28) MUTATED	47	27	20	25
AMP PEAK 30(XQ28) WILD-TYPE	137	60	104	55

Figure S188. Get High-res Image Gene #30: 'amp_xq28' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.11' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S189. Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 1(1P36.11) MUTATED	12	39	13	10
DEL PEAK 1(1P36.11) WILD-TYPE	29	11	21	19

Figure S189. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S190. Gene #31: 'del_1p36.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 1(1P36.11) MUTATED	14	43	17
DEL PEAK 1(1P36.11) WILD-TYPE	33	13	34

Figure S190. Get High-res Image Gene #31: '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 = 8.2e-05

Table S191. Gene #31: 'del_1p36.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 1(1P36.11) MUTATED	26	24	16	9	140	13
DEL PEAK 1(1P36.11) WILD-TYPE	17	91	13	78	29	45

Figure S191. Get High-res Image Gene #31: '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 = 8.2e-05

Table S192. Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 1(1P36.11) MUTATED	28	70	37	26
DEL PEAK 1(1P36.11) WILD-TYPE	62	25	20	99

Figure S192. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.11' versus 'RPPA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S193. Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 1(1P36.11) MUTATED	45	40	57	12
DEL PEAK 1(1P36.11) WILD-TYPE	60	69	29	14

Figure S193. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p36.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.034

Table S194. Gene #31: 'del_1p36.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 1(1P36.11) MUTATED	41	36	21	36	11	9
DEL PEAK 1(1P36.11) WILD-TYPE	38	31	41	24	19	19

Figure S194. Get High-res Image Gene #31: '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 = 8.2e-05

Table S195. Gene #31: 'del_1p36.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 1(1P36.11) MUTATED	29	119	55	24
DEL PEAK 1(1P36.11) WILD-TYPE	77	31	104	59

Figure S195. Get High-res Image Gene #31: '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 = 8.2e-05

Table S196. Gene #31: 'del_1p36.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 1(1P36.11) MUTATED	46	140	41
DEL PEAK 1(1P36.11) WILD-TYPE	132	49	90

Figure S196. Get High-res Image Gene #31: '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 = 8.2e-05

Table S197. Gene #31: 'del_1p36.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 1(1P36.11) MUTATED	94	33	32	57
DEL PEAK 1(1P36.11) WILD-TYPE	90	54	92	23

Figure S197. Get High-res Image Gene #31: '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 = 8.2e-05

Table S198. Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 1(1P36.11) MUTATED	66	52	83	15
DEL PEAK 1(1P36.11) WILD-TYPE	23	66	116	54

Figure S198. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p36.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S199. Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 1(1P36.11) MUTATED	17	59	13	55
DEL PEAK 1(1P36.11) WILD-TYPE	44	56	53	37

Figure S199. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p36.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S200. Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 1(1P36.11) MUTATED	8	100	36
DEL PEAK 1(1P36.11) WILD-TYPE	29	88	73

Figure S200. Get High-res Image Gene #31: 'del_1p36.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p13.1' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S201. Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 2(1P13.1) MUTATED	17	36	10	9
DEL PEAK 2(1P13.1) WILD-TYPE	24	14	24	20

Figure S201. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p13.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S202. Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 2(1P13.1) MUTATED	19	39	14
DEL PEAK 2(1P13.1) WILD-TYPE	28	17	37

Figure S202. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S203. Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 2(1P13.1) MUTATED	24	24	13	17	123	20
DEL PEAK 2(1P13.1) WILD-TYPE	19	91	16	70	46	38

Figure S203. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S204. Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 2(1P13.1) MUTATED	31	60	37	29
DEL PEAK 2(1P13.1) WILD-TYPE	59	35	20	96

Figure S204. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p13.1' versus 'RPPA_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.002

Table S205. Gene #32: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 2(1P13.1) MUTATED	39	41	55	10
DEL PEAK 2(1P13.1) WILD-TYPE	66	68	31	16

Figure S205. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S206. Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 2(1P13.1) MUTATED	32	106	57	25
DEL PEAK 2(1P13.1) WILD-TYPE	74	44	102	58

Figure S206. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S207. Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 2(1P13.1) MUTATED	48	125	47
DEL PEAK 2(1P13.1) WILD-TYPE	130	64	84

Figure S207. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S208. Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 2(1P13.1) MUTATED	90	36	29	55
DEL PEAK 2(1P13.1) WILD-TYPE	94	51	95	25

Figure S208. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S209. Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 2(1P13.1) MUTATED	62	53	79	16
DEL PEAK 2(1P13.1) WILD-TYPE	27	65	120	53

Figure S209. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S210. Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 2(1P13.1) MUTATED	20	58	15	49
DEL PEAK 2(1P13.1) WILD-TYPE	41	57	51	43

Figure S210. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_1p13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S211. Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 2(1P13.1) MUTATED	9	97	36
DEL PEAK 2(1P13.1) WILD-TYPE	28	91	73

Figure S211. Get High-res Image Gene #32: 'del_1p13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2p25.3' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.027

Table S212. Gene #33: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 3(2P25.3) MUTATED	10	7	3	5	15	10
DEL PEAK 3(2P25.3) WILD-TYPE	33	108	26	82	154	48

Figure S212. Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.079

Table S213. Gene #33: 'del_2p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 3(2P25.3) MUTATED	10	3	5	11	2	0
DEL PEAK 3(2P25.3) WILD-TYPE	69	64	57	49	28	28

Figure S213. Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2p25.3' versus 'MIRSEQ_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S214. Gene #33: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 3(2P25.3) MUTATED	28	9	5	6
DEL PEAK 3(2P25.3) WILD-TYPE	156	78	119	74

Figure S214. Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0282 (Fisher's exact test), Q value = 0.056

Table S215. Gene #33: 'del_2p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 3(2P25.3) MUTATED	2	23	4
DEL PEAK 3(2P25.3) WILD-TYPE	35	165	105

Figure S215. Get High-res Image Gene #33: 'del_2p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q22.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S216. Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 4(2Q22.1) MUTATED	10	14	4	16	63	24
DEL PEAK 4(2Q22.1) WILD-TYPE	33	101	25	71	106	34

Figure S216. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q22.1' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S217. Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 4(2Q22.1) MUTATED	25	25	26	16
DEL PEAK 4(2Q22.1) WILD-TYPE	65	70	31	109

Figure S217. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q22.1' versus 'RPPA_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.088

Table S218. Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 4(2Q22.1) MUTATED	17	29	26	3
DEL PEAK 4(2Q22.1) WILD-TYPE	88	80	60	23

Figure S218. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q22.1' versus 'MRNASEQ_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0077

Table S219. Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 4(2Q22.1) MUTATED	22	49	49	11
DEL PEAK 4(2Q22.1) WILD-TYPE	84	101	110	72

Figure S219. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.018

Table S220. Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 4(2Q22.1) MUTATED	33	62	36
DEL PEAK 4(2Q22.1) WILD-TYPE	145	127	95

Figure S220. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_CNMF'

P value = 0.00165 (Fisher's exact test), Q value = 0.0053

Table S221. Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 4(2Q22.1) MUTATED	60	20	19	28
DEL PEAK 4(2Q22.1) WILD-TYPE	124	67	105	52

Figure S221. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.0021

Table S222. Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 4(2Q22.1) MUTATED	35	38	45	9
DEL PEAK 4(2Q22.1) WILD-TYPE	54	80	154	60

Figure S222. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S223. Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 4(2Q22.1) MUTATED	14	41	6	24
DEL PEAK 4(2Q22.1) WILD-TYPE	47	74	60	68

Figure S223. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q22.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.016

Table S224. Gene #34: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 4(2Q22.1) MUTATED	8	60	17
DEL PEAK 4(2Q22.1) WILD-TYPE	29	128	92

Figure S224. Get High-res Image Gene #34: 'del_2q22.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_2q37.1' versus 'MRNA_CNMF'

P value = 0.0016 (Fisher's exact test), Q value = 0.0052

Table S225. Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 5(2Q37.1) MUTATED	7	26	7	10
DEL PEAK 5(2Q37.1) WILD-TYPE	34	24	27	19

Figure S225. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S226. Gene #35: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 5(2Q37.1) MUTATED	11	29	10
DEL PEAK 5(2Q37.1) WILD-TYPE	36	27	41

Figure S226. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S227. Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 5(2Q37.1) MUTATED	12	18	5	15	86	23
DEL PEAK 5(2Q37.1) WILD-TYPE	31	97	24	72	83	35

Figure S227. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S228. Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 5(2Q37.1) MUTATED	28	49	23	20
DEL PEAK 5(2Q37.1) WILD-TYPE	62	46	34	105

Figure S228. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.1' versus 'RPPA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.013

Table S229. Gene #35: 'del_2q37.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 5(2Q37.1) MUTATED	26	29	40	6
DEL PEAK 5(2Q37.1) WILD-TYPE	79	80	46	20

Figure S229. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S230. Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 5(2Q37.1) MUTATED	32	71	44	11
DEL PEAK 5(2Q37.1) WILD-TYPE	74	79	115	72

Figure S230. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S231. Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 5(2Q37.1) MUTATED	38	88	32
DEL PEAK 5(2Q37.1) WILD-TYPE	140	101	99

Figure S231. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S232. Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 5(2Q37.1) MUTATED	75	31	16	31
DEL PEAK 5(2Q37.1) WILD-TYPE	109	56	108	49

Figure S232. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S233. Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 5(2Q37.1) MUTATED	34	54	56	9
DEL PEAK 5(2Q37.1) WILD-TYPE	55	64	143	60

Figure S233. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S234. Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 5(2Q37.1) MUTATED	17	46	8	35
DEL PEAK 5(2Q37.1) WILD-TYPE	44	69	58	57

Figure S234. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S235. Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 5(2Q37.1) MUTATED	3	72	31
DEL PEAK 5(2Q37.1) WILD-TYPE	34	116	78

Figure S235. Get High-res Image Gene #35: 'del_2q37.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p25.3' versus 'MRNA_CNMF'

P value = 0.0402 (Fisher's exact test), Q value = 0.077

Table S236. Gene #36: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 6(3P25.3) MUTATED	30	45	23	25
DEL PEAK 6(3P25.3) WILD-TYPE	11	5	11	4

Figure S236. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p25.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S237. Gene #36: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 6(3P25.3) MUTATED	37	70	25	72	150	44
DEL PEAK 6(3P25.3) WILD-TYPE	6	45	4	15	19	14

Figure S237. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p25.3' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.0011

Table S238. Gene #36: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 6(3P25.3) MUTATED	76	84	49	83
DEL PEAK 6(3P25.3) WILD-TYPE	14	11	8	42

Figure S238. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00271 (Fisher's exact test), Q value = 0.0079

Table S239. Gene #36: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 6(3P25.3) MUTATED	83	131	127	55
DEL PEAK 6(3P25.3) WILD-TYPE	23	19	32	28

Figure S239. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.0015

Table S240. Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 6(3P25.3) MUTATED	141	165	90
DEL PEAK 6(3P25.3) WILD-TYPE	37	24	41

Figure S240. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.012

Table S241. Gene #36: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 6(3P25.3) MUTATED	147	76	85	68
DEL PEAK 6(3P25.3) WILD-TYPE	37	11	39	12

Figure S241. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S242. Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 6(3P25.3) MUTATED	76	94	166	40
DEL PEAK 6(3P25.3) WILD-TYPE	13	24	33	29

Figure S242. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p25.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.027

Table S243. Gene #36: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 6(3P25.3) MUTATED	47	97	43	78
DEL PEAK 6(3P25.3) WILD-TYPE	14	18	23	14

Figure S243. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.024 (Fisher's exact test), Q value = 0.049

Table S244. Gene #36: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 6(3P25.3) MUTATED	30	158	77
DEL PEAK 6(3P25.3) WILD-TYPE	7	30	32

Figure S244. Get High-res Image Gene #36: 'del_3p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p13' versus 'MRNA_CNMF'

P value = 0.0439 (Fisher's exact test), Q value = 0.082

Table S245. Gene #37: 'del_3p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 7(3P13) MUTATED	37	45	24	27
DEL PEAK 7(3P13) WILD-TYPE	4	5	10	2

Figure S245. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S246. Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 7(3P13) MUTATED	41	70	28	81	161	53
DEL PEAK 7(3P13) WILD-TYPE	2	45	1	6	8	5

Figure S246. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p13' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S247. Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 7(3P13) MUTATED	82	88	56	92
DEL PEAK 7(3P13) WILD-TYPE	8	7	1	33

Figure S247. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p13' versus 'RPPA_CHIERARCHICAL'

P value = 0.0448 (Fisher's exact test), Q value = 0.083

Table S248. Gene #37: 'del_3p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 7(3P13) MUTATED	68	59	57	55	24	19
DEL PEAK 7(3P13) WILD-TYPE	11	8	5	5	6	9

Figure S248. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p13' versus 'MRNASEQ_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0024

Table S249. Gene #37: 'del_3p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 7(3P13) MUTATED	95	138	138	60
DEL PEAK 7(3P13) WILD-TYPE	11	12	21	23

Figure S249. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-04 (Fisher's exact test), Q value = 0.003

Table S250. Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 7(3P13) MUTATED	154	175	102
DEL PEAK 7(3P13) WILD-TYPE	24	14	29

Figure S250. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S251. Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 7(3P13) MUTATED	168	82	91	70
DEL PEAK 7(3P13) WILD-TYPE	16	5	33	10

Figure S251. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S252. Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 7(3P13) MUTATED	79	104	185	43
DEL PEAK 7(3P13) WILD-TYPE	10	14	14	26

Figure S252. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S253. Gene #37: 'del_3p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 7(3P13) MUTATED	54	108	44	85
DEL PEAK 7(3P13) WILD-TYPE	7	7	22	7

Figure S253. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00146 (Fisher's exact test), Q value = 0.0048

Table S254. Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 7(3P13) MUTATED	32	174	85
DEL PEAK 7(3P13) WILD-TYPE	5	14	24

Figure S254. Get High-res Image Gene #37: 'del_3p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S255. Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 8(3P12.3) MUTATED	41	67	28	81	158	52
DEL PEAK 8(3P12.3) WILD-TYPE	2	48	1	6	11	6

Figure S255. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S256. Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 8(3P12.3) MUTATED	83	84	56	89
DEL PEAK 8(3P12.3) WILD-TYPE	7	11	1	36

Figure S256. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00577 (Fisher's exact test), Q value = 0.015

Table S257. Gene #38: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 8(3P12.3) MUTATED	65	58	57	55	24	17
DEL PEAK 8(3P12.3) WILD-TYPE	14	9	5	5	6	11

Figure S257. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S258. Gene #38: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 8(3P12.3) MUTATED	94	136	136	58
DEL PEAK 8(3P12.3) WILD-TYPE	12	14	23	25

Figure S258. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0046 (Fisher's exact test), Q value = 0.012

Table S259. Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 8(3P12.3) MUTATED	152	171	101
DEL PEAK 8(3P12.3) WILD-TYPE	26	18	30

Figure S259. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0048

Table S260. Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 8(3P12.3) MUTATED	163	80	92	69
DEL PEAK 8(3P12.3) WILD-TYPE	21	7	32	11

Figure S260. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S261. Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 8(3P12.3) MUTATED	79	103	180	42
DEL PEAK 8(3P12.3) WILD-TYPE	10	15	19	27

Figure S261. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S262. Gene #38: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 8(3P12.3) MUTATED	53	106	44	83
DEL PEAK 8(3P12.3) WILD-TYPE	8	9	22	9

Figure S262. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00236 (Fisher's exact test), Q value = 0.0071

Table S263. Gene #38: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 8(3P12.3) MUTATED	32	171	83
DEL PEAK 8(3P12.3) WILD-TYPE	5	17	26

Figure S263. Get High-res Image Gene #38: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p12.3' versus 'MRNA_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.069

Table S264. Gene #39: 'del_3p12.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 9(3P12.3) MUTATED	36	44	23	27
DEL PEAK 9(3P12.3) WILD-TYPE	5	6	11	2

Figure S264. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S265. Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 9(3P12.3) MUTATED	41	66	27	79	157	51
DEL PEAK 9(3P12.3) WILD-TYPE	2	49	2	8	12	7

Figure S265. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p12.3' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S266. Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 9(3P12.3) MUTATED	81	83	56	88
DEL PEAK 9(3P12.3) WILD-TYPE	9	12	1	37

Figure S266. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p12.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00751 (Fisher's exact test), Q value = 0.019

Table S267. Gene #39: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 9(3P12.3) MUTATED	64	57	57	54	23	17
DEL PEAK 9(3P12.3) WILD-TYPE	15	10	5	6	7	11

Figure S267. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p12.3' versus 'MRNASEQ_CNMF'

P value = 0.00216 (Fisher's exact test), Q value = 0.0067

Table S268. Gene #39: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 9(3P12.3) MUTATED	92	134	134	58
DEL PEAK 9(3P12.3) WILD-TYPE	14	16	25	25

Figure S268. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00757 (Fisher's exact test), Q value = 0.019

Table S269. Gene #39: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 9(3P12.3) MUTATED	149	169	100
DEL PEAK 9(3P12.3) WILD-TYPE	29	20	31

Figure S269. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.0051

Table S270. Gene #39: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 9(3P12.3) MUTATED	160	79	90	69
DEL PEAK 9(3P12.3) WILD-TYPE	24	8	34	11

Figure S270. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S271. Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 9(3P12.3) MUTATED	79	101	176	42
DEL PEAK 9(3P12.3) WILD-TYPE	10	17	23	27

Figure S271. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p12.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 5e-04

Table S272. Gene #39: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 9(3P12.3) MUTATED	53	105	43	82
DEL PEAK 9(3P12.3) WILD-TYPE	8	10	23	10

Figure S272. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p12.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00369 (Fisher's exact test), Q value = 0.01

Table S273. Gene #39: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 9(3P12.3) MUTATED	32	169	82
DEL PEAK 9(3P12.3) WILD-TYPE	5	19	27

Figure S273. Get High-res Image Gene #39: 'del_3p12.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p15.2' versus 'MRNA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00068

Table S274. Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 11(4P15.2) MUTATED	31	39	12	15
DEL PEAK 11(4P15.2) WILD-TYPE	10	11	22	14

Figure S274. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p15.2' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S275. Gene #41: 'del_4p15.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 11(4P15.2) MUTATED	34	44	19
DEL PEAK 11(4P15.2) WILD-TYPE	13	12	32

Figure S275. Get High-res Image Gene #41: '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 = 8.2e-05

Table S276. Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 11(4P15.2) MUTATED	31	46	15	50	138	36
DEL PEAK 11(4P15.2) WILD-TYPE	12	69	14	37	31	22

Figure S276. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p15.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.0013

Table S277. Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 11(4P15.2) MUTATED	58	71	42	60
DEL PEAK 11(4P15.2) WILD-TYPE	32	24	15	65

Figure S277. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p15.2' versus 'RPPA_CNMF'

P value = 0.0285 (Fisher's exact test), Q value = 0.056

Table S278. Gene #41: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 11(4P15.2) MUTATED	62	72	68	18
DEL PEAK 11(4P15.2) WILD-TYPE	43	37	18	8

Figure S278. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p15.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.083

Table S279. Gene #41: 'del_4p15.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 11(4P15.2) MUTATED	52	49	45	45	16	13
DEL PEAK 11(4P15.2) WILD-TYPE	27	18	17	15	14	15

Figure S279. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p15.2' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S280. Gene #41: 'del_4p15.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 11(4P15.2) MUTATED	69	115	86	45
DEL PEAK 11(4P15.2) WILD-TYPE	37	35	73	38

Figure S280. Get High-res Image Gene #41: '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 = 8.2e-05

Table S281. Gene #41: 'del_4p15.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 11(4P15.2) MUTATED	105	147	63
DEL PEAK 11(4P15.2) WILD-TYPE	73	42	68

Figure S281. Get High-res Image Gene #41: '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 = 8.2e-05

Table S282. Gene #41: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 11(4P15.2) MUTATED	134	60	56	53
DEL PEAK 11(4P15.2) WILD-TYPE	50	27	68	27

Figure S282. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.003

Table S283. Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 11(4P15.2) MUTATED	37	79	28	67
DEL PEAK 11(4P15.2) WILD-TYPE	24	36	38	25

Figure S283. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p15.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0025

Table S284. Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 11(4P15.2) MUTATED	17	135	59
DEL PEAK 11(4P15.2) WILD-TYPE	20	53	50

Figure S284. Get High-res Image Gene #41: 'del_4p15.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q22.1' versus 'MRNA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.0022

Table S285. Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 12(4Q22.1) MUTATED	29	37	11	17
DEL PEAK 12(4Q22.1) WILD-TYPE	12	13	23	12

Figure S285. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q22.1' versus 'MRNA_CHIERARCHICAL'

P value = 0.00422 (Fisher's exact test), Q value = 0.012

Table S286. Gene #42: 'del_4q22.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 12(4Q22.1) MUTATED	31	41	22
DEL PEAK 12(4Q22.1) WILD-TYPE	16	15	29

Figure S286. Get High-res Image Gene #42: '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 = 8.2e-05

Table S287. Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 12(4Q22.1) MUTATED	31	44	8	45	128	29
DEL PEAK 12(4Q22.1) WILD-TYPE	12	71	21	42	41	29

Figure S287. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q22.1' versus 'METHLYATION_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.089

Table S288. Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 12(4Q22.1) MUTATED	47	62	34	59
DEL PEAK 12(4Q22.1) WILD-TYPE	43	33	23	66

Figure S288. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q22.1' versus 'RPPA_CNMF'

P value = 0.0281 (Fisher's exact test), Q value = 0.056

Table S289. Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 12(4Q22.1) MUTATED	63	54	60	13
DEL PEAK 12(4Q22.1) WILD-TYPE	42	55	26	13

Figure S289. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q22.1' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S290. Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 12(4Q22.1) MUTATED	58	107	85	33
DEL PEAK 12(4Q22.1) WILD-TYPE	48	43	74	50

Figure S290. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.033

Table S291. Gene #42: 'del_4q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 12(4Q22.1) MUTATED	97	122	64
DEL PEAK 12(4Q22.1) WILD-TYPE	81	67	67

Figure S291. Get High-res Image Gene #42: '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 = 8.2e-05

Table S292. Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 12(4Q22.1) MUTATED	119	47	49	57
DEL PEAK 12(4Q22.1) WILD-TYPE	65	40	75	23

Figure S292. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00613 (Fisher's exact test), Q value = 0.016

Table S293. Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 12(4Q22.1) MUTATED	61	67	116	28
DEL PEAK 12(4Q22.1) WILD-TYPE	28	51	83	41

Figure S293. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q22.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0032

Table S294. Gene #42: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 12(4Q22.1) MUTATED	34	69	22	59
DEL PEAK 12(4Q22.1) WILD-TYPE	27	46	44	33

Figure S294. Get High-res Image Gene #42: 'del_4q22.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q32.3' versus 'MRNA_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0038

Table S295. Gene #43: 'del_4q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 13(4Q32.3) MUTATED	28	41	14	22
DEL PEAK 13(4Q32.3) WILD-TYPE	13	9	20	7

Figure S295. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q32.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.038

Table S296. Gene #43: 'del_4q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 13(4Q32.3) MUTATED	32	45	28
DEL PEAK 13(4Q32.3) WILD-TYPE	15	11	23

Figure S296. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q32.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S297. Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 13(4Q32.3) MUTATED	30	52	11	49	146	41
DEL PEAK 13(4Q32.3) WILD-TYPE	13	63	18	38	23	17

Figure S297. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q32.3' versus 'METHLYATION_CNMF'

P value = 0.00685 (Fisher's exact test), Q value = 0.017

Table S298. Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 13(4Q32.3) MUTATED	60	71	41	67
DEL PEAK 13(4Q32.3) WILD-TYPE	30	24	16	58

Figure S298. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q32.3' versus 'RPPA_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.057

Table S299. Gene #43: 'del_4q32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 13(4Q32.3) MUTATED	65	67	68	16
DEL PEAK 13(4Q32.3) WILD-TYPE	40	42	18	10

Figure S299. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q32.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.0188 (Fisher's exact test), Q value = 0.04

Table S300. Gene #43: 'del_4q32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 13(4Q32.3) MUTATED	56	44	41	47	13	15
DEL PEAK 13(4Q32.3) WILD-TYPE	23	23	21	13	17	13

Figure S300. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q32.3' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S301. Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 13(4Q32.3) MUTATED	69	121	97	40
DEL PEAK 13(4Q32.3) WILD-TYPE	37	29	62	43

Figure S301. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q32.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S302. Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 13(4Q32.3) MUTATED	110	144	73
DEL PEAK 13(4Q32.3) WILD-TYPE	68	45	58

Figure S302. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S303. Gene #43: 'del_4q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 13(4Q32.3) MUTATED	130	65	57	62
DEL PEAK 13(4Q32.3) WILD-TYPE	54	22	67	18

Figure S303. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q32.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00255 (Fisher's exact test), Q value = 0.0076

Table S304. Gene #43: 'del_4q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 13(4Q32.3) MUTATED	66	75	140	33
DEL PEAK 13(4Q32.3) WILD-TYPE	23	43	59	36

Figure S304. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q32.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S305. Gene #43: 'del_4q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 13(4Q32.3) MUTATED	38	80	29	71
DEL PEAK 13(4Q32.3) WILD-TYPE	23	35	37	21

Figure S305. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q32.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S306. Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 13(4Q32.3) MUTATED	25	139	54
DEL PEAK 13(4Q32.3) WILD-TYPE	12	49	55

Figure S306. Get High-res Image Gene #43: 'del_4q32.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S307. Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 14(4Q35.2) MUTATED	30	56	10	51	146	38
DEL PEAK 14(4Q35.2) WILD-TYPE	13	59	19	36	23	20

Figure S307. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.024

Table S308. Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 14(4Q35.2) MUTATED	60	72	39	68
DEL PEAK 14(4Q35.2) WILD-TYPE	30	23	18	57

Figure S308. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S309. Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 14(4Q35.2) MUTATED	66	121	101	41
DEL PEAK 14(4Q35.2) WILD-TYPE	40	29	58	42

Figure S309. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00325 (Fisher's exact test), Q value = 0.0092

Table S310. Gene #44: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 14(4Q35.2) MUTATED	113	141	75
DEL PEAK 14(4Q35.2) WILD-TYPE	65	48	56

Figure S310. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S311. Gene #44: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 14(4Q35.2) MUTATED	130	63	57	64
DEL PEAK 14(4Q35.2) WILD-TYPE	54	24	67	16

Figure S311. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.02

Table S312. Gene #44: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 14(4Q35.2) MUTATED	67	74	138	35
DEL PEAK 14(4Q35.2) WILD-TYPE	22	44	61	34

Figure S312. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00108 (Fisher's exact test), Q value = 0.0037

Table S313. Gene #44: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 14(4Q35.2) MUTATED	41	81	29	67
DEL PEAK 14(4Q35.2) WILD-TYPE	20	34	37	25

Figure S313. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0011 (Fisher's exact test), Q value = 0.0038

Table S314. Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 14(4Q35.2) MUTATED	26	136	56
DEL PEAK 14(4Q35.2) WILD-TYPE	11	52	53

Figure S314. Get High-res Image Gene #44: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q12.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S315. Gene #45: 'del_5q12.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 15(5Q12.1) MUTATED	30	52	28	71	143	45
DEL PEAK 15(5Q12.1) WILD-TYPE	13	63	1	16	26	13

Figure S315. Get High-res Image Gene #45: '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 = 8.2e-05

Table S316. Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 15(5Q12.1) MUTATED	78	78	41	71
DEL PEAK 15(5Q12.1) WILD-TYPE	12	17	16	54

Figure S316. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q12.1' versus 'MRNASEQ_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.0027

Table S317. Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 15(5Q12.1) MUTATED	72	125	119	50
DEL PEAK 15(5Q12.1) WILD-TYPE	34	25	40	33

Figure S317. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q12.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00132 (Fisher's exact test), Q value = 0.0044

Table S318. Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 15(5Q12.1) MUTATED	131	153	82
DEL PEAK 15(5Q12.1) WILD-TYPE	47	36	49

Figure S318. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S319. Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 15(5Q12.1) MUTATED	66	82	167	38
DEL PEAK 15(5Q12.1) WILD-TYPE	23	36	32	31

Figure S319. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q12.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00064

Table S320. Gene #45: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 15(5Q12.1) MUTATED	47	97	35	66
DEL PEAK 15(5Q12.1) WILD-TYPE	14	18	31	26

Figure S320. Get High-res Image Gene #45: 'del_5q12.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S321. Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 16(5Q31.1) MUTATED	35	56	29	75	142	49
DEL PEAK 16(5Q31.1) WILD-TYPE	8	59	0	12	27	9

Figure S321. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q31.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S322. Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 16(5Q31.1) MUTATED	85	81	43	75
DEL PEAK 16(5Q31.1) WILD-TYPE	5	14	14	50

Figure S322. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q31.1' versus 'MRNASEQ_CNMF'

P value = 0.00723 (Fisher's exact test), Q value = 0.018

Table S323. Gene #46: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 16(5Q31.1) MUTATED	79	128	121	55
DEL PEAK 16(5Q31.1) WILD-TYPE	27	22	38	28

Figure S323. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q31.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00649 (Fisher's exact test), Q value = 0.017

Table S324. Gene #46: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 16(5Q31.1) MUTATED	137	157	89
DEL PEAK 16(5Q31.1) WILD-TYPE	41	32	42

Figure S324. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.034

Table S325. Gene #46: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 16(5Q31.1) MUTATED	146	76	86	60
DEL PEAK 16(5Q31.1) WILD-TYPE	38	11	38	20

Figure S325. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q31.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S326. Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 16(5Q31.1) MUTATED	69	90	171	38
DEL PEAK 16(5Q31.1) WILD-TYPE	20	28	28	31

Figure S326. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q31.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S327. Gene #46: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 16(5Q31.1) MUTATED	50	100	38	70
DEL PEAK 16(5Q31.1) WILD-TYPE	11	15	28	22

Figure S327. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q31.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.044

Table S328. Gene #46: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 16(5Q31.1) MUTATED	31	153	74
DEL PEAK 16(5Q31.1) WILD-TYPE	6	35	35

Figure S328. Get High-res Image Gene #46: 'del_5q31.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S329. Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 17(6P25.3) MUTATED	14	24	13	14	62	7
DEL PEAK 17(6P25.3) WILD-TYPE	29	91	16	73	107	51

Figure S329. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S330. Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 17(6P25.3) MUTATED	17	45	18	24
DEL PEAK 17(6P25.3) WILD-TYPE	73	50	39	101

Figure S330. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S331. Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 17(6P25.3) MUTATED	28	63	23	19
DEL PEAK 17(6P25.3) WILD-TYPE	78	87	136	64

Figure S331. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S332. Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 17(6P25.3) MUTATED	37	78	18
DEL PEAK 17(6P25.3) WILD-TYPE	141	111	113

Figure S332. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6p25.3' versus 'MIRSEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.074

Table S333. Gene #47: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 17(6P25.3) MUTATED	42	23	31	32
DEL PEAK 17(6P25.3) WILD-TYPE	142	64	93	48

Figure S333. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0031

Table S334. Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 17(6P25.3) MUTATED	39	32	45	12
DEL PEAK 17(6P25.3) WILD-TYPE	50	86	154	57

Figure S334. Get High-res Image Gene #47: 'del_6p25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q26' versus 'MRNA_CHIERARCHICAL'

P value = 0.00525 (Fisher's exact test), Q value = 0.014

Table S335. Gene #48: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 18(6Q26) MUTATED	11	23	7
DEL PEAK 18(6Q26) WILD-TYPE	36	33	44

Figure S335. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q26' versus 'CN_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.012

Table S336. Gene #48: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 18(6Q26) MUTATED	13	21	6	19	64	12
DEL PEAK 18(6Q26) WILD-TYPE	30	94	23	68	105	46

Figure S336. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0055

Table S337. Gene #48: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 18(6Q26) MUTATED	21	34	24	23
DEL PEAK 18(6Q26) WILD-TYPE	69	61	33	102

Figure S337. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q26' versus 'MRNASEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0038

Table S338. Gene #48: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 18(6Q26) MUTATED	23	59	35	17
DEL PEAK 18(6Q26) WILD-TYPE	83	91	124	66

Figure S338. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q26' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00814 (Fisher's exact test), Q value = 0.02

Table S339. Gene #48: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 18(6Q26) MUTATED	39	66	29
DEL PEAK 18(6Q26) WILD-TYPE	139	123	102

Figure S339. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q26' versus 'MIRSEQ_CNMF'

P value = 0.0278 (Fisher's exact test), Q value = 0.055

Table S340. Gene #48: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 18(6Q26) MUTATED	57	22	22	27
DEL PEAK 18(6Q26) WILD-TYPE	127	65	102	53

Figure S340. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0027

Table S341. Gene #48: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 18(6Q26) MUTATED	13	33	7	35
DEL PEAK 18(6Q26) WILD-TYPE	48	82	59	57

Figure S341. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_6q26' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0439 (Fisher's exact test), Q value = 0.082

Table S342. Gene #48: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 18(6Q26) MUTATED	9	59	20
DEL PEAK 18(6Q26) WILD-TYPE	28	129	89

Figure S342. Get High-res Image Gene #48: 'del_6q26' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q11.22' versus 'CN_CNMF'

P value = 0.00961 (Fisher's exact test), Q value = 0.023

Table S343. Gene #49: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 19(7Q11.22) MUTATED	4	6	2	9	13	14
DEL PEAK 19(7Q11.22) WILD-TYPE	39	109	27	78	156	44

Figure S343. Get High-res Image Gene #49: 'del_7q11.22' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q11.22' versus 'MRNASEQ_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0029

Table S344. Gene #49: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 19(7Q11.22) MUTATED	6	7	28	7
DEL PEAK 19(7Q11.22) WILD-TYPE	100	143	131	76

Figure S344. Get High-res Image Gene #49: 'del_7q11.22' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q11.22' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0037

Table S345. Gene #49: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 19(7Q11.22) MUTATED	12	12	24
DEL PEAK 19(7Q11.22) WILD-TYPE	166	177	107

Figure S345. Get High-res Image Gene #49: 'del_7q11.22' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0489 (Fisher's exact test), Q value = 0.089

Table S346. Gene #50: 'del_7q36.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 20(7Q36.3) MUTATED	14	6	11
DEL PEAK 20(7Q36.3) WILD-TYPE	33	50	40

Figure S346. Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.3' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0012

Table S347. Gene #50: 'del_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 20(7Q36.3) MUTATED	14	26	8	13	21	22
DEL PEAK 20(7Q36.3) WILD-TYPE	29	89	21	74	148	36

Figure S347. Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.3' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00089

Table S348. Gene #50: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 20(7Q36.3) MUTATED	25	18	49	12
DEL PEAK 20(7Q36.3) WILD-TYPE	81	132	110	71

Figure S348. Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0043

Table S349. Gene #50: 'del_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 20(7Q36.3) MUTATED	44	24	36
DEL PEAK 20(7Q36.3) WILD-TYPE	134	165	95

Figure S349. Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00442 (Fisher's exact test), Q value = 0.012

Table S350. Gene #50: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 20(7Q36.3) MUTATED	14	29	49	5
DEL PEAK 20(7Q36.3) WILD-TYPE	75	89	150	64

Figure S350. Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.002

Table S351. Gene #50: 'del_7q36.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 20(7Q36.3) MUTATED	14	45	11
DEL PEAK 20(7Q36.3) WILD-TYPE	23	143	98

Figure S351. Get High-res Image Gene #50: 'del_7q36.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S352. Gene #51: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 21(8P23.2) MUTATED	36	57	19	57	127	45
DEL PEAK 21(8P23.2) WILD-TYPE	7	58	10	30	42	13

Figure S352. Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.051

Table S353. Gene #51: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 21(8P23.2) MUTATED	62	71	43	72
DEL PEAK 21(8P23.2) WILD-TYPE	28	24	14	53

Figure S353. Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.034

Table S354. Gene #51: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 21(8P23.2) MUTATED	132	64	70	58
DEL PEAK 21(8P23.2) WILD-TYPE	52	23	54	22

Figure S354. Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.034

Table S355. Gene #51: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 21(8P23.2) MUTATED	29	133	62
DEL PEAK 21(8P23.2) WILD-TYPE	8	55	47

Figure S355. Get High-res Image Gene #51: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.033

Table S356. Gene #52: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 22(9P23) MUTATED	35	29	20	17
DEL PEAK 22(9P23) WILD-TYPE	6	21	14	12

Figure S356. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0052

Table S357. Gene #52: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 22(9P23) MUTATED	40	30	31
DEL PEAK 22(9P23) WILD-TYPE	7	26	20

Figure S357. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S358. Gene #52: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 22(9P23) MUTATED	33	54	25	75	105	40
DEL PEAK 22(9P23) WILD-TYPE	10	61	4	12	64	18

Figure S358. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 0.00217 (Fisher's exact test), Q value = 0.0067

Table S359. Gene #52: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 22(9P23) MUTATED	74	58	37	75
DEL PEAK 22(9P23) WILD-TYPE	16	37	20	50

Figure S359. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S360. Gene #52: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 22(9P23) MUTATED	83	87	115	44
DEL PEAK 22(9P23) WILD-TYPE	23	63	44	39

Figure S360. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0035

Table S361. Gene #52: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 22(9P23) MUTATED	136	112	81
DEL PEAK 22(9P23) WILD-TYPE	42	77	50

Figure S361. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0032

Table S362. Gene #52: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 22(9P23) MUTATED	132	68	74	43
DEL PEAK 22(9P23) WILD-TYPE	52	19	50	37

Figure S362. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00098

Table S363. Gene #52: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 22(9P23) MUTATED	50	81	151	35
DEL PEAK 22(9P23) WILD-TYPE	39	37	48	34

Figure S363. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S364. Gene #52: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 22(9P23) MUTATED	45	90	28	60
DEL PEAK 22(9P23) WILD-TYPE	16	25	38	32

Figure S364. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.043

Table S365. Gene #52: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 22(9P23) MUTATED	30	130	63
DEL PEAK 22(9P23) WILD-TYPE	7	58	46

Figure S365. Get High-res Image Gene #52: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S366. Gene #53: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 23(9P21.3) MUTATED	37	63	27	81	135	45
DEL PEAK 23(9P21.3) WILD-TYPE	6	52	2	6	34	13

Figure S366. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.0055

Table S367. Gene #53: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 23(9P21.3) MUTATED	93	111	127	54
DEL PEAK 23(9P21.3) WILD-TYPE	13	39	32	29

Figure S367. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.034

Table S368. Gene #53: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 23(9P21.3) MUTATED	150	141	94
DEL PEAK 23(9P21.3) WILD-TYPE	28	48	37

Figure S368. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.028

Table S369. Gene #53: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 23(9P21.3) MUTATED	68	95	165	44
DEL PEAK 23(9P21.3) WILD-TYPE	21	23	34	25

Figure S369. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0033

Table S370. Gene #53: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 23(9P21.3) MUTATED	53	99	41	69
DEL PEAK 23(9P21.3) WILD-TYPE	8	16	25	23

Figure S370. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0373 (Fisher's exact test), Q value = 0.072

Table S371. Gene #53: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 23(9P21.3) MUTATED	34	149	79
DEL PEAK 23(9P21.3) WILD-TYPE	3	39	30

Figure S371. Get High-res Image Gene #53: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S372. Gene #54: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 24(9P21.1) MUTATED	28	55	25	77	102	39
DEL PEAK 24(9P21.1) WILD-TYPE	15	60	4	10	67	19

Figure S372. Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.1' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0011

Table S373. Gene #54: 'del_9p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 24(9P21.1) MUTATED	83	85	111	44
DEL PEAK 24(9P21.1) WILD-TYPE	23	65	48	39

Figure S373. Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.0016

Table S374. Gene #54: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 24(9P21.1) MUTATED	135	106	82
DEL PEAK 24(9P21.1) WILD-TYPE	43	83	49

Figure S374. Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00918 (Fisher's exact test), Q value = 0.022

Table S375. Gene #54: 'del_9p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 24(9P21.1) MUTATED	51	84	140	36
DEL PEAK 24(9P21.1) WILD-TYPE	38	34	59	33

Figure S375. Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00138 (Fisher's exact test), Q value = 0.0046

Table S376. Gene #54: 'del_9p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 24(9P21.1) MUTATED	45	88	33	56
DEL PEAK 24(9P21.1) WILD-TYPE	16	27	33	36

Figure S376. Get High-res Image Gene #54: 'del_9p21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S377. Gene #55: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 25(9Q21.11) MUTATED	27	13	20	15
DEL PEAK 25(9Q21.11) WILD-TYPE	14	37	14	14

Figure S377. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S378. Gene #55: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 25(9Q21.11) MUTATED	31	14	30
DEL PEAK 25(9Q21.11) WILD-TYPE	16	42	21

Figure S378. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S379. Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 25(9Q21.11) MUTATED	27	50	20	60	52	42
DEL PEAK 25(9Q21.11) WILD-TYPE	16	65	9	27	117	16

Figure S379. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S380. Gene #55: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 25(9Q21.11) MUTATED	66	23	27	68
DEL PEAK 25(9Q21.11) WILD-TYPE	24	72	30	57

Figure S380. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.045

Table S381. Gene #55: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 25(9Q21.11) MUTATED	31	29	41	35	16	15
DEL PEAK 25(9Q21.11) WILD-TYPE	48	38	21	25	14	13

Figure S381. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S382. Gene #55: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 25(9Q21.11) MUTATED	68	36	104	41
DEL PEAK 25(9Q21.11) WILD-TYPE	38	114	55	42

Figure S382. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S383. Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 25(9Q21.11) MUTATED	125	46	78
DEL PEAK 25(9Q21.11) WILD-TYPE	53	143	53

Figure S383. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S384. Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 25(9Q21.11) MUTATED	85	60	69	23
DEL PEAK 25(9Q21.11) WILD-TYPE	99	27	55	57

Figure S384. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S385. Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 25(9Q21.11) MUTATED	23	54	129	31
DEL PEAK 25(9Q21.11) WILD-TYPE	66	64	70	38

Figure S385. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.0091

Table S386. Gene #55: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 25(9Q21.11) MUTATED	42	61	24	46
DEL PEAK 25(9Q21.11) WILD-TYPE	19	54	42	46

Figure S386. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0151 (Fisher's exact test), Q value = 0.034

Table S387. Gene #55: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 25(9Q21.11) MUTATED	27	96	50
DEL PEAK 25(9Q21.11) WILD-TYPE	10	92	59

Figure S387. Get High-res Image Gene #55: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S388. Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 26(10P15.3) MUTATED	21	34	17	27	103	26
DEL PEAK 26(10P15.3) WILD-TYPE	22	81	12	60	66	32

Figure S388. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S389. Gene #56: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 26(10P15.3) MUTATED	34	60	35	42
DEL PEAK 26(10P15.3) WILD-TYPE	56	35	22	83

Figure S389. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S390. Gene #56: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 26(10P15.3) MUTATED	37	95	69	26
DEL PEAK 26(10P15.3) WILD-TYPE	69	55	90	57

Figure S390. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.0012

Table S391. Gene #56: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 26(10P15.3) MUTATED	71	108	48
DEL PEAK 26(10P15.3) WILD-TYPE	107	81	83

Figure S391. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S392. Gene #56: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 26(10P15.3) MUTATED	96	40	35	50
DEL PEAK 26(10P15.3) WILD-TYPE	88	47	89	30

Figure S392. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S393. Gene #56: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 26(10P15.3) MUTATED	63	45	97	16
DEL PEAK 26(10P15.3) WILD-TYPE	26	73	102	53

Figure S393. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S394. Gene #56: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 26(10P15.3) MUTATED	26	63	14	49
DEL PEAK 26(10P15.3) WILD-TYPE	35	52	52	43

Figure S394. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10p15.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.083

Table S395. Gene #56: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 26(10P15.3) MUTATED	18	95	39
DEL PEAK 26(10P15.3) WILD-TYPE	19	93	70

Figure S395. Get High-res Image Gene #56: 'del_10p15.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S396. Gene #57: 'del_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 27(10P15.1) MUTATED	17	29	16	27	99	23
DEL PEAK 27(10P15.1) WILD-TYPE	26	86	13	60	70	35

Figure S396. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S397. Gene #57: 'del_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 27(10P15.1) MUTATED	31	57	34	35
DEL PEAK 27(10P15.1) WILD-TYPE	59	38	23	90

Figure S397. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S398. Gene #57: 'del_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 27(10P15.1) MUTATED	34	92	63	21
DEL PEAK 27(10P15.1) WILD-TYPE	72	58	96	62

Figure S398. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 4e-04

Table S399. Gene #57: 'del_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 27(10P15.1) MUTATED	62	103	45
DEL PEAK 27(10P15.1) WILD-TYPE	116	86	86

Figure S399. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10p15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S400. Gene #57: 'del_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 27(10P15.1) MUTATED	85	36	31	52
DEL PEAK 27(10P15.1) WILD-TYPE	99	51	93	28

Figure S400. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S401. Gene #57: 'del_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 27(10P15.1) MUTATED	62	39	89	14
DEL PEAK 27(10P15.1) WILD-TYPE	27	79	110	55

Figure S401. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S402. Gene #57: 'del_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 27(10P15.1) MUTATED	23	56	13	45
DEL PEAK 27(10P15.1) WILD-TYPE	38	59	53	47

Figure S402. Get High-res Image Gene #57: 'del_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 0.00975 (Fisher's exact test), Q value = 0.024

Table S403. Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 28(10Q23.31) MUTATED	17	36	15	13
DEL PEAK 28(10Q23.31) WILD-TYPE	24	14	19	16

Figure S403. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 0.00116 (Fisher's exact test), Q value = 0.004

Table S404. Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 28(10Q23.31) MUTATED	17	40	24
DEL PEAK 28(10Q23.31) WILD-TYPE	30	16	27

Figure S404. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S405. Gene #58: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 28(10Q23.31) MUTATED	26	39	13	41	127	22
DEL PEAK 28(10Q23.31) WILD-TYPE	17	76	16	46	42	36

Figure S405. Get High-res Image Gene #58: '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 = 8.2e-05

Table S406. Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 28(10Q23.31) MUTATED	43	69	38	48
DEL PEAK 28(10Q23.31) WILD-TYPE	47	26	19	77

Figure S406. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.08

Table S407. Gene #58: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 28(10Q23.31) MUTATED	39	34	36	40	10	12
DEL PEAK 28(10Q23.31) WILD-TYPE	40	33	26	20	20	16

Figure S407. Get High-res Image Gene #58: '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 = 8.2e-05

Table S408. Gene #58: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 28(10Q23.31) MUTATED	46	114	72	35
DEL PEAK 28(10Q23.31) WILD-TYPE	60	36	87	48

Figure S408. Get High-res Image Gene #58: '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 = 8.2e-05

Table S409. Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 28(10Q23.31) MUTATED	78	135	54
DEL PEAK 28(10Q23.31) WILD-TYPE	100	54	77

Figure S409. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0011

Table S410. Gene #58: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 28(10Q23.31) MUTATED	100	49	49	56
DEL PEAK 28(10Q23.31) WILD-TYPE	84	38	75	24

Figure S410. Get High-res Image Gene #58: '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 = 8.2e-05

Table S411. Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 28(10Q23.31) MUTATED	64	51	112	27
DEL PEAK 28(10Q23.31) WILD-TYPE	25	67	87	42

Figure S411. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S412. Gene #58: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 28(10Q23.31) MUTATED	28	73	20	58
DEL PEAK 28(10Q23.31) WILD-TYPE	33	42	46	34

Figure S412. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S413. Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 28(10Q23.31) MUTATED	20	113	46
DEL PEAK 28(10Q23.31) WILD-TYPE	17	75	63

Figure S413. Get High-res Image Gene #58: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0068

Table S414. Gene #59: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 29(11P15.5) MUTATED	29	19	12	18
DEL PEAK 29(11P15.5) WILD-TYPE	12	31	22	11

Figure S414. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.026

Table S415. Gene #59: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 29(11P15.5) MUTATED	32	22	24
DEL PEAK 29(11P15.5) WILD-TYPE	15	34	27

Figure S415. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S416. Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 29(11P15.5) MUTATED	31	30	13	53	79	39
DEL PEAK 29(11P15.5) WILD-TYPE	12	85	16	34	90	19

Figure S416. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S417. Gene #59: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 29(11P15.5) MUTATED	60	43	27	46
DEL PEAK 29(11P15.5) WILD-TYPE	30	52	30	79

Figure S417. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 0.00855 (Fisher's exact test), Q value = 0.021

Table S418. Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 29(11P15.5) MUTATED	35	28	41	34	15	8
DEL PEAK 29(11P15.5) WILD-TYPE	44	39	21	26	15	20

Figure S418. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 0.00795 (Fisher's exact test), Q value = 0.02

Table S419. Gene #59: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 29(11P15.5) MUTATED	59	66	89	30
DEL PEAK 29(11P15.5) WILD-TYPE	47	84	70	53

Figure S419. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0027

Table S420. Gene #59: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 29(11P15.5) MUTATED	110	45	53	28
DEL PEAK 29(11P15.5) WILD-TYPE	74	42	71	52

Figure S420. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00288 (Fisher's exact test), Q value = 0.0083

Table S421. Gene #59: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 29(11P15.5) MUTATED	35	62	19	48
DEL PEAK 29(11P15.5) WILD-TYPE	26	53	47	44

Figure S421. Get High-res Image Gene #59: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11q22.1' versus 'CN_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.0024

Table S422. Gene #60: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 30(11Q22.1) MUTATED	10	27	11	19	68	28
DEL PEAK 30(11Q22.1) WILD-TYPE	33	88	18	68	101	30

Figure S422. Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q22.1' versus 'METHLYATION_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0055

Table S423. Gene #60: 'del_11q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 30(11Q22.1) MUTATED	36	39	25	27
DEL PEAK 30(11Q22.1) WILD-TYPE	54	56	32	98

Figure S423. Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q22.1' versus 'MRNASEQ_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.047

Table S424. Gene #60: 'del_11q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 30(11Q22.1) MUTATED	31	61	52	18
DEL PEAK 30(11Q22.1) WILD-TYPE	75	89	107	65

Figure S424. Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q22.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0296 (Fisher's exact test), Q value = 0.058

Table S425. Gene #60: 'del_11q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 30(11Q22.1) MUTATED	49	75	38
DEL PEAK 30(11Q22.1) WILD-TYPE	129	114	93

Figure S425. Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q22.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.041

Table S426. Gene #60: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 30(11Q22.1) MUTATED	39	40	64	14
DEL PEAK 30(11Q22.1) WILD-TYPE	50	78	135	55

Figure S426. Get High-res Image Gene #60: 'del_11q22.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q25' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S427. Gene #61: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 31(11Q25) MUTATED	8	33	13	23	80	27
DEL PEAK 31(11Q25) WILD-TYPE	35	82	16	64	89	31

Figure S427. Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q25' versus 'METHLYATION_CNMF'

P value = 0.0169 (Fisher's exact test), Q value = 0.036

Table S428. Gene #61: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 31(11Q25) MUTATED	32	39	30	36
DEL PEAK 31(11Q25) WILD-TYPE	58	56	27	89

Figure S428. Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q25' versus 'MRNASEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.068

Table S429. Gene #61: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 31(11Q25) MUTATED	33	65	63	22
DEL PEAK 31(11Q25) WILD-TYPE	73	85	96	61

Figure S429. Get High-res Image Gene #61: 'del_11q25' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S430. Gene #63: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 33(13Q12.11) MUTATED	34	57	14	71	111	44
DEL PEAK 33(13Q12.11) WILD-TYPE	9	58	15	16	58	14

Figure S430. Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q12.11' versus 'METHLYATION_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.078

Table S431. Gene #63: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 33(13Q12.11) MUTATED	64	69	37	70
DEL PEAK 33(13Q12.11) WILD-TYPE	26	26	20	55

Figure S431. Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q12.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.028

Table S432. Gene #63: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 33(13Q12.11) MUTATED	21	138	64
DEL PEAK 33(13Q12.11) WILD-TYPE	16	50	45

Figure S432. Get High-res Image Gene #63: 'del_13q12.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S433. Gene #64: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 34(13Q14.2) MUTATED	34	62	13	73	118	44
DEL PEAK 34(13Q14.2) WILD-TYPE	9	53	16	14	51	14

Figure S433. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.051

Table S434. Gene #64: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 34(13Q14.2) MUTATED	65	72	39	72
DEL PEAK 34(13Q14.2) WILD-TYPE	25	23	18	53

Figure S434. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.033

Table S435. Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 34(13Q14.2) MUTATED	42	87	35	67
DEL PEAK 34(13Q14.2) WILD-TYPE	19	28	31	25

Figure S435. Get High-res Image Gene #64: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MRNA_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.014

Table S436. Gene #65: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 35(14Q11.2) MUTATED	5	21	14	12
DEL PEAK 35(14Q11.2) WILD-TYPE	36	29	20	17

Figure S436. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.0335 (Fisher's exact test), Q value = 0.065

Table S437. Gene #65: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 35(14Q11.2) MUTATED	9	22	21
DEL PEAK 35(14Q11.2) WILD-TYPE	38	34	30

Figure S437. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q11.2' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S438. Gene #65: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 35(14Q11.2) MUTATED	5	29	8	37	67	29
DEL PEAK 35(14Q11.2) WILD-TYPE	38	86	21	50	102	29

Figure S438. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q11.2' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00045

Table S439. Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 35(14Q11.2) MUTATED	22	56	73	22
DEL PEAK 35(14Q11.2) WILD-TYPE	84	94	86	61

Figure S439. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S440. Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 35(14Q11.2) MUTATED	43	69	61
DEL PEAK 35(14Q11.2) WILD-TYPE	135	120	70

Figure S440. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00995 (Fisher's exact test), Q value = 0.024

Table S441. Gene #65: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 35(14Q11.2) MUTATED	42	42	67	15
DEL PEAK 35(14Q11.2) WILD-TYPE	47	76	132	54

Figure S441. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.0092

Table S442. Gene #65: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 35(14Q11.2) MUTATED	11	52	22	35
DEL PEAK 35(14Q11.2) WILD-TYPE	50	63	44	57

Figure S442. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0024 (Fisher's exact test), Q value = 0.0072

Table S443. Gene #65: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 35(14Q11.2) MUTATED	6	81	33
DEL PEAK 35(14Q11.2) WILD-TYPE	31	107	76

Figure S443. Get High-res Image Gene #65: 'del_14q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S444. Gene #66: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 36(15Q11.2) MUTATED	27	39	6	16	52	27
DEL PEAK 36(15Q11.2) WILD-TYPE	16	76	23	71	117	31

Figure S444. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q11.2' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.037

Table S445. Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 36(15Q11.2) MUTATED	76	30	32	21
DEL PEAK 36(15Q11.2) WILD-TYPE	108	57	92	59

Figure S445. Get High-res Image Gene #66: 'del_15q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S446. Gene #67: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 37(15Q21.1) MUTATED	26	35	8	15	55	30
DEL PEAK 37(15Q21.1) WILD-TYPE	17	80	21	72	114	28

Figure S446. Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q21.1' versus 'MIRSEQ_CNMF'

P value = 0.00128 (Fisher's exact test), Q value = 0.0043

Table S447. Gene #67: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 37(15Q21.1) MUTATED	77	34	28	21
DEL PEAK 37(15Q21.1) WILD-TYPE	107	53	96	59

Figure S447. Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0283 (Fisher's exact test), Q value = 0.056

Table S448. Gene #67: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 37(15Q21.1) MUTATED	19	41	12	36
DEL PEAK 37(15Q21.1) WILD-TYPE	42	74	54	56

Figure S448. Get High-res Image Gene #67: 'del_15q21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16p13.3' versus 'CN_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.001

Table S449. Gene #68: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 38(16P13.3) MUTATED	14	26	11	32	70	34
DEL PEAK 38(16P13.3) WILD-TYPE	29	89	18	55	99	24

Figure S449. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16p13.3' versus 'METHLYATION_CNMF'

P value = 0.00979 (Fisher's exact test), Q value = 0.024

Table S450. Gene #68: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 38(16P13.3) MUTATED	43	34	28	36
DEL PEAK 38(16P13.3) WILD-TYPE	47	61	29	89

Figure S450. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.038

Table S451. Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 38(16P13.3) MUTATED	76	38	32	31
DEL PEAK 38(16P13.3) WILD-TYPE	108	49	92	49

Figure S451. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.007

Table S452. Gene #68: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 38(16P13.3) MUTATED	25	51	12	38
DEL PEAK 38(16P13.3) WILD-TYPE	36	64	54	54

Figure S452. Get High-res Image Gene #68: 'del_16p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'CN_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.077

Table S453. Gene #69: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 39(16Q23.1) MUTATED	16	34	12	40	82	26
DEL PEAK 39(16Q23.1) WILD-TYPE	27	81	17	47	87	32

Figure S453. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q23.1' versus 'RPPA_CNMF'

P value = 0.007 (Fisher's exact test), Q value = 0.018

Table S454. Gene #69: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 39(16Q23.1) MUTATED	43	41	50	7
DEL PEAK 39(16Q23.1) WILD-TYPE	62	68	36	19

Figure S454. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q23.1' versus 'MRNASEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.084

Table S455. Gene #69: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 39(16Q23.1) MUTATED	37	70	74	27
DEL PEAK 39(16Q23.1) WILD-TYPE	69	80	85	56

Figure S455. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.072

Table S456. Gene #69: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 39(16Q23.1) MUTATED	61	88	59
DEL PEAK 39(16Q23.1) WILD-TYPE	117	101	72

Figure S456. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q23.1' versus 'MIRSEQ_CNMF'

P value = 0.00463 (Fisher's exact test), Q value = 0.012

Table S457. Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 39(16Q23.1) MUTATED	80	46	37	38
DEL PEAK 39(16Q23.1) WILD-TYPE	104	41	87	42

Figure S457. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0131 (Fisher's exact test), Q value = 0.03

Table S458. Gene #69: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 39(16Q23.1) MUTATED	21	59	19	42
DEL PEAK 39(16Q23.1) WILD-TYPE	40	56	47	50

Figure S458. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0032

Table S459. Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 39(16Q23.1) MUTATED	10	96	35
DEL PEAK 39(16Q23.1) WILD-TYPE	27	92	74

Figure S459. Get High-res Image Gene #69: 'del_16q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S460. Gene #70: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 40(17P11.2) MUTATED	31	38	14	63	93	33
DEL PEAK 40(17P11.2) WILD-TYPE	12	77	15	24	76	25

Figure S460. Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.035

Table S461. Gene #70: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 40(17P11.2) MUTATED	112	92	67
DEL PEAK 40(17P11.2) WILD-TYPE	66	97	64

Figure S461. Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.052

Table S462. Gene #70: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 40(17P11.2) MUTATED	42	67	122	30
DEL PEAK 40(17P11.2) WILD-TYPE	47	51	77	39

Figure S462. Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 0.03

Table S463. Gene #70: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 40(17P11.2) MUTATED	31	60	28	62
DEL PEAK 40(17P11.2) WILD-TYPE	30	55	38	30

Figure S463. Get High-res Image Gene #70: 'del_17p11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q11.2' versus 'MRNA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.0016

Table S464. Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 41(17Q11.2) MUTATED	20	5	11	7
DEL PEAK 41(17Q11.2) WILD-TYPE	21	45	23	22

Figure S464. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S465. Gene #71: 'del_17q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 41(17Q11.2) MUTATED	21	5	17
DEL PEAK 41(17Q11.2) WILD-TYPE	26	51	34

Figure S465. Get High-res Image Gene #71: '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 = 8.2e-05

Table S466. Gene #71: 'del_17q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 41(17Q11.2) MUTATED	22	28	11	34	17	20
DEL PEAK 41(17Q11.2) WILD-TYPE	21	87	18	53	152	38

Figure S466. Get High-res Image Gene #71: '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 = 8.2e-05

Table S467. Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 41(17Q11.2) MUTATED	34	9	11	38
DEL PEAK 41(17Q11.2) WILD-TYPE	56	86	46	87

Figure S467. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q11.2' versus 'RPPA_CNMF'

P value = 0.0052 (Fisher's exact test), Q value = 0.014

Table S468. Gene #71: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 41(17Q11.2) MUTATED	29	36	11	9
DEL PEAK 41(17Q11.2) WILD-TYPE	76	73	75	17

Figure S468. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.017

Table S469. Gene #71: 'del_17q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	79	67	62	60	30	28
DEL PEAK 41(17Q11.2) MUTATED	21	11	28	11	7	7
DEL PEAK 41(17Q11.2) WILD-TYPE	58	56	34	49	23	21

Figure S469. Get High-res Image Gene #71: '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 = 8.2e-05

Table S470. Gene #71: 'del_17q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 41(17Q11.2) MUTATED	40	13	52	26
DEL PEAK 41(17Q11.2) WILD-TYPE	66	137	107	57

Figure S470. Get High-res Image Gene #71: '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 = 8.2e-05

Table S471. Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 41(17Q11.2) MUTATED	74	19	38
DEL PEAK 41(17Q11.2) WILD-TYPE	104	170	93

Figure S471. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0045

Table S472. Gene #71: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 41(17Q11.2) MUTATED	12	27	64	25
DEL PEAK 41(17Q11.2) WILD-TYPE	77	91	135	44

Figure S472. Get High-res Image Gene #71: 'del_17q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MRNA_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.055

Table S473. Gene #72: 'del_17q25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 42(17Q25.3) MUTATED	14	5	8	4
DEL PEAK 42(17Q25.3) WILD-TYPE	27	45	26	25

Figure S473. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q25.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.026

Table S474. Gene #72: 'del_17q25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 42(17Q25.3) MUTATED	15	5	11
DEL PEAK 42(17Q25.3) WILD-TYPE	32	51	40

Figure S474. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q25.3' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S475. Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 42(17Q25.3) MUTATED	14	20	7	32	16	13
DEL PEAK 42(17Q25.3) WILD-TYPE	29	95	22	55	153	45

Figure S475. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q25.3' versus 'MRNASEQ_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0088

Table S476. Gene #72: 'del_17q25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 42(17Q25.3) MUTATED	32	18	37	15
DEL PEAK 42(17Q25.3) WILD-TYPE	74	132	122	68

Figure S476. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q25.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0043

Table S477. Gene #72: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 42(17Q25.3) MUTATED	51	25	26
DEL PEAK 42(17Q25.3) WILD-TYPE	127	164	105

Figure S477. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q25.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.03

Table S478. Gene #72: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 42(17Q25.3) MUTATED	8	28	48	15
DEL PEAK 42(17Q25.3) WILD-TYPE	81	90	151	54

Figure S478. Get High-res Image Gene #72: 'del_17q25.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.005

Table S479. Gene #73: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 43(18Q23) MUTATED	31	39	15	40	80	29
DEL PEAK 43(18Q23) WILD-TYPE	12	76	14	47	89	29

Figure S479. Get High-res Image Gene #73: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.018

Table S480. Gene #73: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 43(18Q23) MUTATED	23	52	26	57
DEL PEAK 43(18Q23) WILD-TYPE	38	63	40	35

Figure S480. Get High-res Image Gene #73: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S481. Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 44(19P13.3) MUTATED	27	34	14	50	72	39
DEL PEAK 44(19P13.3) WILD-TYPE	16	81	15	37	97	19

Figure S481. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.045

Table S482. Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 44(19P13.3) MUTATED	86	76	73
DEL PEAK 44(19P13.3) WILD-TYPE	92	113	58

Figure S482. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.055

Table S483. Gene #74: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 44(19P13.3) MUTATED	99	45	49	31
DEL PEAK 44(19P13.3) WILD-TYPE	85	42	75	49

Figure S483. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0031

Table S484. Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 44(19P13.3) MUTATED	30	57	112	25
DEL PEAK 44(19P13.3) WILD-TYPE	59	61	87	44

Figure S484. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.011

Table S485. Gene #74: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 44(19P13.3) MUTATED	30	63	18	41
DEL PEAK 44(19P13.3) WILD-TYPE	31	52	48	51

Figure S485. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00426 (Fisher's exact test), Q value = 0.012

Table S486. Gene #74: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 44(19P13.3) MUTATED	21	95	36
DEL PEAK 44(19P13.3) WILD-TYPE	16	93	73

Figure S486. Get High-res Image Gene #74: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S487. Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 45(19Q13.32) MUTATED	18	13	9	22	73	14
DEL PEAK 45(19Q13.32) WILD-TYPE	25	102	20	65	96	44

Figure S487. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.0054

Table S488. Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 45(19Q13.32) MUTATED	30	36	20	21
DEL PEAK 45(19Q13.32) WILD-TYPE	60	59	37	104

Figure S488. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.032

Table S489. Gene #75: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 45(19Q13.32) MUTATED	33	24	37	6
DEL PEAK 45(19Q13.32) WILD-TYPE	72	85	49	20

Figure S489. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.038

Table S490. Gene #75: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 45(19Q13.32) MUTATED	26	60	41	22
DEL PEAK 45(19Q13.32) WILD-TYPE	80	90	118	61

Figure S490. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.018

Table S491. Gene #75: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 45(19Q13.32) MUTATED	42	72	35
DEL PEAK 45(19Q13.32) WILD-TYPE	136	117	96

Figure S491. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.012

Table S492. Gene #75: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 45(19Q13.32) MUTATED	65	26	22	28
DEL PEAK 45(19Q13.32) WILD-TYPE	119	61	102	52

Figure S492. Get High-res Image Gene #75: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0032

Table S493. Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 46(21Q11.2) MUTATED	19	40	19	37	93	36
DEL PEAK 46(21Q11.2) WILD-TYPE	24	75	10	50	76	22

Figure S493. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.039

Table S494. Gene #76: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 46(21Q11.2) MUTATED	45	56	31	48
DEL PEAK 46(21Q11.2) WILD-TYPE	45	39	26	77

Figure S494. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00019

Table S495. Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 46(21Q11.2) MUTATED	106	52	41	34
DEL PEAK 46(21Q11.2) WILD-TYPE	78	35	83	46

Figure S495. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00025

Table S496. Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 46(21Q11.2) MUTATED	42	66	108	17
DEL PEAK 46(21Q11.2) WILD-TYPE	47	52	91	52

Figure S496. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0049

Table S497. Gene #76: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 46(21Q11.2) MUTATED	29	68	19	47
DEL PEAK 46(21Q11.2) WILD-TYPE	32	47	47	45

Figure S497. Get High-res Image Gene #76: 'del_21q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_21q22.3' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00014

Table S498. Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 47(21Q22.3) MUTATED	25	42	22	41	111	40
DEL PEAK 47(21Q22.3) WILD-TYPE	18	73	7	46	58	18

Figure S498. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q22.3' versus 'METHLYATION_CNMF'

P value = 0.00399 (Fisher's exact test), Q value = 0.011

Table S499. Gene #77: 'del_21q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 47(21Q22.3) MUTATED	51	61	35	52
DEL PEAK 47(21Q22.3) WILD-TYPE	39	34	22	73

Figure S499. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S500. Gene #77: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 47(21Q22.3) MUTATED	119	55	52	43
DEL PEAK 47(21Q22.3) WILD-TYPE	65	32	72	37

Figure S500. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_21q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S501. Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 47(21Q22.3) MUTATED	55	70	121	23
DEL PEAK 47(21Q22.3) WILD-TYPE	34	48	78	46

Figure S501. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.055

Table S502. Gene #77: 'del_21q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 47(21Q22.3) MUTATED	31	67	25	55
DEL PEAK 47(21Q22.3) WILD-TYPE	30	48	41	37

Figure S502. Get High-res Image Gene #77: 'del_21q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_22q11.21' versus 'CN_CNMF'

P value = 0.00776 (Fisher's exact test), Q value = 0.019

Table S503. Gene #78: 'del_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 48(22Q11.21) MUTATED	7	27	0	24	27	10
DEL PEAK 48(22Q11.21) WILD-TYPE	36	88	29	63	142	48

Figure S503. Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00098

Table S504. Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 48(22Q11.21) MUTATED	23	31	41
DEL PEAK 48(22Q11.21) WILD-TYPE	155	158	90

Figure S504. Get High-res Image Gene #78: 'del_22q11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MRNA_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.002

Table S505. Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 49(22Q13.32) MUTATED	7	7	10	16
DEL PEAK 49(22Q13.32) WILD-TYPE	34	43	24	13

Figure S505. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_22q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.025

Table S506. Gene #79: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 49(22Q13.32) MUTATED	10	9	21
DEL PEAK 49(22Q13.32) WILD-TYPE	37	47	30

Figure S506. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_22q13.32' versus 'CN_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00068

Table S507. Gene #79: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 49(22Q13.32) MUTATED	10	33	0	29	33	22
DEL PEAK 49(22Q13.32) WILD-TYPE	33	82	29	58	136	36

Figure S507. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'RPPA_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.081

Table S508. Gene #79: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 49(22Q13.32) MUTATED	24	36	22	2
DEL PEAK 49(22Q13.32) WILD-TYPE	81	73	64	24

Figure S508. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_22q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S509. Gene #79: 'del_22q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 49(22Q13.32) MUTATED	28	23	59	17
DEL PEAK 49(22Q13.32) WILD-TYPE	78	127	100	66

Figure S509. Get High-res Image Gene #79: '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 = 8.2e-05

Table S510. Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 49(22Q13.32) MUTATED	38	30	59
DEL PEAK 49(22Q13.32) WILD-TYPE	140	159	72

Figure S510. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_22q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0022

Table S511. Gene #79: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 49(22Q13.32) MUTATED	11	37	59	10
DEL PEAK 49(22Q13.32) WILD-TYPE	78	81	140	59

Figure S511. Get High-res Image Gene #79: 'del_22q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp22.2' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00072

Table S512. Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 50(XP22.2) MUTATED	12	18	9	28	72	16
DEL PEAK 50(XP22.2) WILD-TYPE	31	97	20	59	97	42

Figure S512. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp22.2' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S513. Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 50(XP22.2) MUTATED	37	40	15	21
DEL PEAK 50(XP22.2) WILD-TYPE	53	55	42	104

Figure S513. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp22.2' versus 'MRNASEQ_CNMF'

P value = 0.00461 (Fisher's exact test), Q value = 0.012

Table S514. Gene #80: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 50(XP22.2) MUTATED	33	60	45	15
DEL PEAK 50(XP22.2) WILD-TYPE	73	90	114	68

Figure S514. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp22.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00982 (Fisher's exact test), Q value = 0.024

Table S515. Gene #80: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 50(XP22.2) MUTATED	49	73	31
DEL PEAK 50(XP22.2) WILD-TYPE	129	116	100

Figure S515. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp22.2' versus 'MIRSEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.05

Table S516. Gene #80: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 50(XP22.2) MUTATED	55	35	28	30
DEL PEAK 50(XP22.2) WILD-TYPE	129	52	96	50

Figure S516. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.0014

Table S517. Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 50(XP22.2) MUTATED	14	45	9	36
DEL PEAK 50(XP22.2) WILD-TYPE	47	70	57	56

Figure S517. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp22.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00598 (Fisher's exact test), Q value = 0.016

Table S518. Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 50(XP22.2) MUTATED	8	72	24
DEL PEAK 50(XP22.2) WILD-TYPE	29	116	85

Figure S518. Get High-res Image Gene #80: 'del_xp22.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S519. Gene #81: 'del_xp21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 51(XP21.1) MUTATED	10	14	10	27	75	15
DEL PEAK 51(XP21.1) WILD-TYPE	33	101	19	60	94	43

Figure S519. Get High-res Image Gene #81: '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 = 8.2e-05

Table S520. Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 51(XP21.1) MUTATED	36	40	18	15
DEL PEAK 51(XP21.1) WILD-TYPE	54	55	39	110

Figure S520. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp21.1' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 3e-04

Table S521. Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 51(XP21.1) MUTATED	32	66	36	15
DEL PEAK 51(XP21.1) WILD-TYPE	74	84	123	68

Figure S521. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0025

Table S522. Gene #81: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 51(XP21.1) MUTATED	47	75	27
DEL PEAK 51(XP21.1) WILD-TYPE	131	114	104

Figure S522. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_CNMF'

P value = 0.00143 (Fisher's exact test), Q value = 0.0047

Table S523. Gene #81: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 51(XP21.1) MUTATED	61	31	22	32
DEL PEAK 51(XP21.1) WILD-TYPE	123	56	102	48

Figure S523. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.004

Table S524. Gene #81: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 51(XP21.1) MUTATED	38	40	58	10
DEL PEAK 51(XP21.1) WILD-TYPE	51	78	141	59

Figure S524. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp21.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.0016

Table S525. Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 51(XP21.1) MUTATED	11	46	10	32
DEL PEAK 51(XP21.1) WILD-TYPE	50	69	56	60

Figure S525. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0037

Table S526. Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 51(XP21.1) MUTATED	6	71	22
DEL PEAK 51(XP21.1) WILD-TYPE	31	117	87

Figure S526. Get High-res Image Gene #81: 'del_xp21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp11.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S527. Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 52(XP11.3) MUTATED	11	13	10	26	77	12
DEL PEAK 52(XP11.3) WILD-TYPE	32	102	19	61	92	46

Figure S527. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xp11.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S528. Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 52(XP11.3) MUTATED	34	41	21	12
DEL PEAK 52(XP11.3) WILD-TYPE	56	54	36	113

Figure S528. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xp11.3' versus 'RPPA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.03

Table S529. Gene #82: 'del_xp11.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	105	109	86	26
DEL PEAK 52(XP11.3) MUTATED	28	25	37	10
DEL PEAK 52(XP11.3) WILD-TYPE	77	84	49	16

Figure S529. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_xp11.3' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00035

Table S530. Gene #82: 'del_xp11.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 52(XP11.3) MUTATED	30	65	40	13
DEL PEAK 52(XP11.3) WILD-TYPE	76	85	119	70

Figure S530. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xp11.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.0067

Table S531. Gene #82: 'del_xp11.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	178	189	131
DEL PEAK 52(XP11.3) MUTATED	47	73	28
DEL PEAK 52(XP11.3) WILD-TYPE	131	116	103

Figure S531. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00075

Table S532. Gene #82: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 52(XP11.3) MUTATED	61	28	20	34
DEL PEAK 52(XP11.3) WILD-TYPE	123	59	104	46

Figure S532. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xp11.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.0024

Table S533. Gene #82: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 52(XP11.3) MUTATED	38	38	58	9
DEL PEAK 52(XP11.3) WILD-TYPE	51	80	141	60

Figure S533. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xp11.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0027

Table S534. Gene #82: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 52(XP11.3) MUTATED	12	43	9	33
DEL PEAK 52(XP11.3) WILD-TYPE	49	72	57	59

Figure S534. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xp11.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00095 (Fisher's exact test), Q value = 0.0034

Table S535. Gene #82: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 52(XP11.3) MUTATED	7	70	20
DEL PEAK 52(XP11.3) WILD-TYPE	30	118	89

Figure S535. Get High-res Image Gene #82: 'del_xp11.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xq22.3' versus 'MRNA_CNMF'

P value = 0.00687 (Fisher's exact test), Q value = 0.017

Table S536. Gene #83: 'del_xq22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	41	50	34	29
DEL PEAK 53(XQ22.3) MUTATED	15	7	4	11
DEL PEAK 53(XQ22.3) WILD-TYPE	26	43	30	18

Figure S536. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_xq22.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.025

Table S537. Gene #83: 'del_xq22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	47	56	51
DEL PEAK 53(XQ22.3) MUTATED	18	7	12
DEL PEAK 53(XQ22.3) WILD-TYPE	29	49	39

Figure S537. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_xq22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S538. Gene #83: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	43	115	29	87	169	58
DEL PEAK 53(XQ22.3) MUTATED	14	5	5	39	39	12
DEL PEAK 53(XQ22.3) WILD-TYPE	29	110	24	48	130	46

Figure S538. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_xq22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S539. Gene #83: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	90	95	57	125
DEL PEAK 53(XQ22.3) MUTATED	34	21	19	5
DEL PEAK 53(XQ22.3) WILD-TYPE	56	74	38	120

Figure S539. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_xq22.3' versus 'MRNASEQ_CNMF'

P value = 0.00178 (Fisher's exact test), Q value = 0.0056

Table S540. Gene #83: 'del_xq22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	106	150	159	83
DEL PEAK 53(XQ22.3) MUTATED	33	30	42	8
DEL PEAK 53(XQ22.3) WILD-TYPE	73	120	117	75

Figure S540. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 8.2e-05

Table S541. Gene #83: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	184	87	124	80
DEL PEAK 53(XQ22.3) MUTATED	58	25	10	17
DEL PEAK 53(XQ22.3) WILD-TYPE	126	62	114	63

Figure S541. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_xq22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00059

Table S542. Gene #83: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	89	118	199	69
DEL PEAK 53(XQ22.3) MUTATED	20	33	54	3
DEL PEAK 53(XQ22.3) WILD-TYPE	69	85	145	66

Figure S542. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_xq22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.0013

Table S543. Gene #83: 'del_xq22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	61	115	66	92
DEL PEAK 53(XQ22.3) MUTATED	13	33	3	24
DEL PEAK 53(XQ22.3) WILD-TYPE	48	82	63	68

Figure S543. Get High-res Image Gene #83: 'del_xq22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_xq22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0165 (Fisher's exact test), Q value = 0.036

Table S544. Gene #83: 'del_xq22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	37	188	109
DEL PEAK 53(XQ22.3) MUTATED	10	49	14
DEL PEAK 53(XQ22.3) WILD-TYPE	27	139	95

Figure S544. Get High-res Image Gene #83: 'del_xq22.3' 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/LUSC-TP/22533935/transformed.cor.cli.txt
Molecular subtype file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/22552638/LUSC-TP.transferedmergedcluster.txt
Number of patients = 501
Number of significantly focal cnvs = 83
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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