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

Breast Invasive Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XG9PV5

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 69 focal events and 12 molecular subtypes across 1044 patients, 671 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_1q44 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_3p25.1 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'.
amp_3q26.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_4q13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_5p15.33 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_6p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_6q21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8p11.23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8p11.21 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_8q24.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10p15.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_10q22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11p13 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_11q14.1 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_12p13.33 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_12q15 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_13q34 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_14q21.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_15q26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_17q23.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19p13.12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_19q13.42 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
amp_20q13.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_1p36.13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_1p21.2 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2p25.1 cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_2q37.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_3p21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4p16.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_4q35.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q11.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_5q21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6p25.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q15 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_6q27 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_7p22.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_7q36.1 cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_8p11.21 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p23 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9p21.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q21.11 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_9q34.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_11q13.1 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11q23.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12p13.2 cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_12q23.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_12q24.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_13q14.2 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_14q24.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_15q13.1 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_16q24.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17p12 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_17q21.31 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_18q23 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_19p13.3 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_19q13.32 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_20p13 cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_21q11.2 cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_22q11.1 cnv correlated to 'CN_CNMF'.
del_22q13.32 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 69 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, 671 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1p22 3	244 (23%)	800	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00036 (0.0691)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 3q26 32	331 (32%)	713	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	2e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 6p23	288 (28%)	756	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	4e-05 (0.00972)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 6q21	198 (19%)	846	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 8q24 21	663 (64%)	381	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 10p15 1	294 (28%)	750	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 12p13 33	277 (27%)	767	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 13q34	176 (17%)	868	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 19q12	273 (26%)	771	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 20q13 2	535 (51%)	509	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0006 (0.109)	0.00027 (0.0535)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 2q37 3	310 (30%)	734	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 3p21 31	337 (32%)	707	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 4p16 3	330 (32%)	714	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 4q35 2	337 (32%)	707	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 5q11 2	272 (26%)	772	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 5q21 3	264 (25%)	780	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 9q34 2	293 (28%)	751	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 10q23 31	313 (30%)	731	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 10q26 3	311 (30%)	733	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 11p15 5	302 (29%)	742	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 12q23 1	199 (19%)	845	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 12q24 31	205 (20%)	839	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 14q24 1	341 (33%)	703	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 15q13 1	364 (35%)	680	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	7e-05 (0.016)	4e-05 (0.00972)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 16q24 3	672 (64%)	372	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 17p12	629 (60%)	415	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00071 (0.126)	1e-05 (0.00828)
del 17q21 31	362 (35%)	682	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 19p13 3	350 (34%)	694	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 19q13 32	206 (20%)	838	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00054 (0.0994)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 20p13	156 (15%)	888	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00024 (0.0487)	0.00085 (0.146)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 17q23 1	417 (40%)	627	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.358 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	7e-05 (0.016)	1e-05 (0.00828)
amp 19p13 12	221 (21%)	823	8e-05 (0.0179)	0.00026 (0.052)	1e-05 (0.00828)	5e-05 (0.0117)	0.00089 (0.152)	0.00178 (0.273)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	5e-05 (0.0117)	3e-05 (0.00828)
del 8p23 2	542 (52%)	502	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00877 (0.947)	0.00074 (0.13)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 9p23	319 (31%)	725	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0107 (1.00)	0.00082 (0.142)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00012 (0.0253)	1e-05 (0.00828)
del 9q21 11	289 (28%)	755	0.00115 (0.193)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00749 (0.846)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 13q14 2	485 (46%)	559	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.265 (1.00)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 3p25 1	197 (19%)	847	0.00077 (0.135)	5e-05 (0.0117)	1e-05 (0.00828)	0.00012 (0.0253)	0.241 (1.00)	0.379 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0001 (0.0215)	2e-05 (0.00828)
amp 4q13 3	159 (15%)	885	1e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0463 (1.00)	0.0377 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	6e-05 (0.0137)	1e-05 (0.00828)
amp 11q13 3	386 (37%)	658	0.00024 (0.0487)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.983 (1.00)	0.00062 (0.112)	1e-05 (0.00828)	1e-05 (0.00828)	0.00054 (0.0994)	2e-05 (0.00828)	0.0105 (1.00)	0.00028 (0.0549)
amp 15q26 3	187 (18%)	857	1e-05 (0.00828)	0.00015 (0.0312)	1e-05 (0.00828)	0.00115 (0.193)	0.0022 (0.328)	0.00783 (0.877)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00015 (0.0312)	1e-05 (0.00828)
amp 17q12	320 (31%)	724	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0933 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00118 (0.196)	1e-05 (0.00828)	0.00411 (0.53)	1e-05 (0.00828)
del 7p22 3	134 (13%)	910	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00225 (0.333)	0.00451 (0.55)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
del 8p11 21	199 (19%)	845	0.0001 (0.0215)	0.00026 (0.052)	1e-05 (0.00828)	0.0119 (1.00)	0.0301 (1.00)	0.00017 (0.035)	1e-05 (0.00828)	1e-05 (0.00828)	3e-05 (0.00828)	1e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)
del 9p21 3	357 (34%)	687	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00496 (0.59)	0.00419 (0.536)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)
del 18q23	343 (33%)	701	9e-05 (0.0198)	5e-05 (0.0117)	1e-05 (0.00828)	1e-05 (0.00828)	0.00385 (0.52)	0.0313 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 5p15 33	382 (37%)	662	0.00884 (0.947)	0.00078 (0.136)	1e-05 (0.00828)	1e-05 (0.00828)	0.0472 (1.00)	0.477 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 10q22 3	146 (14%)	898	2e-05 (0.00828)	9e-05 (0.0198)	1e-05 (0.00828)	0.00275 (0.388)	0.00473 (0.572)	0.487 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.00031 (0.0601)	1e-05 (0.00828)	0.00045 (0.0837)	4e-05 (0.00972)
amp 11q14 1	258 (25%)	786	0.00555 (0.644)	9e-05 (0.0198)	1e-05 (0.00828)	9e-05 (0.0198)	0.0834 (1.00)	0.257 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	8e-05 (0.0179)	2e-05 (0.00828)	4e-05 (0.00972)
amp 12q15	269 (26%)	775	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00024 (0.0487)	0.29 (1.00)	0.00479 (0.575)	1e-05 (0.00828)	1e-05 (0.00828)	4e-05 (0.00972)	1e-05 (0.00828)	0.00815 (0.9)	1e-05 (0.00828)
amp 14q21 1	213 (20%)	831	2e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)	4e-05 (0.00972)	0.0691 (1.00)	0.0026 (0.372)	1e-05 (0.00828)	1e-05 (0.00828)	7e-05 (0.016)	1e-05 (0.00828)	0.151 (1.00)	1e-05 (0.00828)
del 11q23 2	534 (51%)	510	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.92 (1.00)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0906 (1.00)	0.0007 (0.125)	0.244 (1.00)	0.00126 (0.205)
amp 1q21 3	757 (73%)	287	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0469 (1.00)	0.0136 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.00211 (0.316)	1e-05 (0.00828)	0.0266 (1.00)	0.00125 (0.205)
amp 11p13	217 (21%)	827	0.164 (1.00)	0.00093 (0.158)	1e-05 (0.00828)	0.00394 (0.527)	0.0625 (1.00)	0.0494 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 19q13 42	268 (26%)	776	0.00044 (0.0823)	0.00255 (0.368)	1e-05 (0.00828)	0.00095 (0.161)	0.00122 (0.201)	0.247 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.00011 (0.0234)	5e-05 (0.0117)	0.121 (1.00)	0.0269 (1.00)
del 1p36 13	437 (42%)	607	7e-05 (0.016)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00338 (0.463)	0.00398 (0.527)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.0102 (1.00)	0.00177 (0.273)
del 1p21 2	345 (33%)	699	0.00425 (0.54)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00031 (0.0601)	0.00161 (0.253)	1e-05 (0.00828)	1e-05 (0.00828)	0.00149 (0.237)	1e-05 (0.00828)	0.388 (1.00)	0.0019 (0.289)
del 6q15	341 (33%)	703	1e-05 (0.00828)	0.00036 (0.0691)	1e-05 (0.00828)	1e-05 (0.00828)	0.454 (1.00)	0.014 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.00195 (0.294)	1e-05 (0.00828)	0.00287 (0.399)	1e-05 (0.00828)
del 7q36 1	195 (19%)	849	0.0025 (0.367)	1e-05 (0.00828)	1e-05 (0.00828)	0.00264 (0.375)	0.31 (1.00)	0.0309 (1.00)	1e-05 (0.00828)	2e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)
amp 8p11 23	399 (38%)	645	1e-05 (0.00828)	1e-05 (0.00828)	1e-05 (0.00828)	0.00014 (0.0293)	0.0543 (1.00)	4e-05 (0.00972)	1e-05 (0.00828)	1e-05 (0.00828)	0.412 (1.00)	0.129 (1.00)	0.46 (1.00)	0.0507 (1.00)
amp 8p11 21	411 (39%)	633	0.0442 (1.00)	0.00425 (0.54)	1e-05 (0.00828)	8e-05 (0.0179)	0.901 (1.00)	0.0768 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.00981 (1.00)	0.0007 (0.125)	0.00145 (0.232)	3e-05 (0.00828)
del 21q11 2	209 (20%)	835	0.00019 (0.0389)	0.00396 (0.527)	1e-05 (0.00828)	0.00027 (0.0535)	0.0614 (1.00)	0.00849 (0.925)	0.00011 (0.0234)	1e-05 (0.00828)	0.00393 (0.527)	4e-05 (0.00972)	0.159 (1.00)	0.00066 (0.119)
amp 1q44	763 (73%)	281	2e-05 (0.00828)	0.00125 (0.205)	1e-05 (0.00828)	0.00436 (0.54)	0.853 (1.00)	0.364 (1.00)	1e-05 (0.00828)	8e-05 (0.0179)	0.82 (1.00)	0.0296 (1.00)	0.214 (1.00)	0.00695 (0.795)
del 2p25 1	198 (19%)	846	0.419 (1.00)	0.382 (1.00)	1e-05 (0.00828)	0.00427 (0.54)	0.184 (1.00)	0.225 (1.00)	0.0204 (1.00)	1e-05 (0.00828)	0.00019 (0.0389)	9e-05 (0.0198)	0.00691 (0.795)	0.00161 (0.253)
del 11q13 1	233 (22%)	811	0.00406 (0.528)	0.00254 (0.368)	1e-05 (0.00828)	5e-05 (0.0117)	0.399 (1.00)	0.0256 (1.00)	1e-05 (0.00828)	1e-05 (0.00828)	0.286 (1.00)	0.00425 (0.54)	0.286 (1.00)	0.0115 (1.00)
del 6p25 3	202 (19%)	842	0.376 (1.00)	0.74 (1.00)	1e-05 (0.00828)	0.00364 (0.495)	0.391 (1.00)	0.0953 (1.00)	0.00144 (0.232)	0.0473 (1.00)	0.199 (1.00)	0.0345 (1.00)	0.0309 (1.00)	0.00039 (0.0741)
del 6q27	362 (35%)	682	0.0219 (1.00)	0.011 (1.00)	1e-05 (0.00828)	0.15 (1.00)	0.0587 (1.00)	0.0644 (1.00)	0.00154 (0.243)	0.00028 (0.0549)	0.472 (1.00)	0.164 (1.00)	0.665 (1.00)	0.683 (1.00)
del 12p13 2	177 (17%)	867	0.035 (1.00)	0.107 (1.00)	0.00046 (0.0851)	0.0336 (1.00)	0.32 (1.00)	0.236 (1.00)	0.00511 (0.603)	0.00167 (0.259)	0.0004 (0.0756)	0.00041 (0.0771)	0.0028 (0.392)	0.00325 (0.448)
del 22q11 1	453 (43%)	591	0.372 (1.00)	0.435 (1.00)	1e-05 (0.00828)	0.023 (1.00)	0.342 (1.00)	0.104 (1.00)	0.42 (1.00)	0.223 (1.00)	0.0908 (1.00)	0.00547 (0.64)	0.402 (1.00)	0.09 (1.00)
del 22q13 32	481 (46%)	563	0.257 (1.00)	0.0106 (1.00)	1e-05 (0.00828)	0.0816 (1.00)	0.173 (1.00)	0.0171 (1.00)	0.0187 (1.00)	0.00252 (0.368)	0.0707 (1.00)	0.00811 (0.9)	0.495 (1.00)	0.106 (1.00)

'amp_1p22.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 1(1P22.3) MUTATED	52	36	31	113	12
AMP PEAK 1(1P22.3) WILD-TYPE	347	204	68	151	30

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

'amp_1p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1p22.3' versus 'RPPA_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.069

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

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

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

'amp_1p22.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 1(1P22.3) MUTATED	99	14	53	36	33	5	2
AMP PEAK 1(1P22.3) WILD-TYPE	91	129	181	125	211	47	14

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

'amp_1p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 1(1P22.3) MUTATED	97	29	35	38	28	15
AMP PEAK 1(1P22.3) WILD-TYPE	81	214	162	142	156	43

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

'amp_1p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 1(1P22.3) MUTATED	50	66	125
AMP PEAK 1(1P22.3) WILD-TYPE	256	356	172

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

'amp_1p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 1(1P22.3) MUTATED	27	27	72	78	37
AMP PEAK 1(1P22.3) WILD-TYPE	147	159	333	56	89

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

'amp_1p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 1(1P22.3) MUTATED	35	42	92
AMP PEAK 1(1P22.3) WILD-TYPE	214	214	117

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

'amp_1p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 1(1P22.3) MUTATED	70	6	39	21	17	16
AMP PEAK 1(1P22.3) WILD-TYPE	57	61	154	114	108	51

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

'amp_1q21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 2(1Q21.3) MUTATED	245	177	97	207	31
AMP PEAK 2(1Q21.3) WILD-TYPE	154	63	2	57	11

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

'amp_1q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_1q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 2(1Q21.3) MUTATED	163	84	196	113	152	35	10
AMP PEAK 2(1Q21.3) WILD-TYPE	27	59	38	48	92	17	6

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

'amp_1q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 2(1Q21.3) MUTATED	155	158	149	139	119	33
AMP PEAK 2(1Q21.3) WILD-TYPE	23	85	48	41	65	25

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

'amp_1q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S19. Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 2(1Q21.3) MUTATED	117	112	301	120	90
AMP PEAK 2(1Q21.3) WILD-TYPE	57	74	104	14	36

Figure S19. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_1q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.2

Table S20. Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 2(1Q21.3) MUTATED	105	41	142	82	90	44
AMP PEAK 2(1Q21.3) WILD-TYPE	22	26	51	53	35	23

Figure S20. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_1q44' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S21. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S21. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_1q44' versus 'MRNA_CHIERARCHICAL'

P value = 0.00125 (Fisher's exact test), Q value = 0.2

Table S22. Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S22. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_1q44' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 3(1Q44) MUTATED	256	180	99	200	28
AMP PEAK 3(1Q44) WILD-TYPE	143	60	0	64	14

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

'amp_1q44' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S24. Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 3(1Q44) MUTATED	146	95	202	118	145	41	12
AMP PEAK 3(1Q44) WILD-TYPE	44	48	32	43	99	11	4

Figure S24. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_1q44' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.018

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 3(1Q44) MUTATED	139	175	152	145	113	35
AMP PEAK 3(1Q44) WILD-TYPE	39	68	45	35	71	23

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

'amp_3p25.1' versus 'MRNA_CNMF'

P value = 0.00077 (Fisher's exact test), Q value = 0.13

Table S26. Gene #4: 'amp_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S26. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3p25.1' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S27. Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S27. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S28. Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 4(3P25.1) MUTATED	20	71	24	72	10
AMP PEAK 4(3P25.1) WILD-TYPE	379	169	75	192	32

Figure S28. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3p25.1' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.025

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

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

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

'amp_3p25.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S30. Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 4(3P25.1) MUTATED	46	9	31	42	61	2	5
AMP PEAK 4(3P25.1) WILD-TYPE	144	134	203	119	183	50	11

Figure S30. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S31. Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 4(3P25.1) MUTATED	43	19	22	58	41	13
AMP PEAK 4(3P25.1) WILD-TYPE	135	224	175	122	143	45

Figure S31. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S32. Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 4(3P25.1) MUTATED	32	82	75
AMP PEAK 4(3P25.1) WILD-TYPE	274	340	222

Figure S32. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S33. Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 4(3P25.1) MUTATED	10	22	90	33	34
AMP PEAK 4(3P25.1) WILD-TYPE	164	164	315	101	92

Figure S33. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.021

Table S34. Gene #4: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 4(3P25.1) MUTATED	45	28	55
AMP PEAK 4(3P25.1) WILD-TYPE	204	228	154

Figure S34. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3p25.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S35. Gene #4: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 4(3P25.1) MUTATED	32	4	44	22	9	17
AMP PEAK 4(3P25.1) WILD-TYPE	95	63	149	113	116	50

Figure S35. Get High-res Image Gene #4: 'amp_3p25.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S36. Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S36. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_3q26.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S37. Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S37. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_3q26.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S38. Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 5(3Q26.32) MUTATED	36	95	29	161	10
AMP PEAK 5(3Q26.32) WILD-TYPE	363	145	70	103	32

Figure S38. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #3: 'CN_CNMF'

'amp_3q26.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S39. Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S39. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_3q26.32' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_3q26.32' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S41. Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S41. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_3q26.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S42. Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 5(3Q26.32) MUTATED	119	20	45	64	68	4	8
AMP PEAK 5(3Q26.32) WILD-TYPE	71	123	189	97	176	48	8

Figure S42. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_3q26.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S43. Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 5(3Q26.32) MUTATED	112	30	35	74	52	25
AMP PEAK 5(3Q26.32) WILD-TYPE	66	213	162	106	132	33

Figure S43. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S44. Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 5(3Q26.32) MUTATED	46	115	161
AMP PEAK 5(3Q26.32) WILD-TYPE	260	307	136

Figure S44. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_3q26.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S45. Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 5(3Q26.32) MUTATED	17	41	120	83	61
AMP PEAK 5(3Q26.32) WILD-TYPE	157	145	285	51	65

Figure S45. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S46. Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 5(3Q26.32) MUTATED	57	44	108
AMP PEAK 5(3Q26.32) WILD-TYPE	192	212	101

Figure S46. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_3q26.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S47. Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 5(3Q26.32) MUTATED	75	8	55	32	13	26
AMP PEAK 5(3Q26.32) WILD-TYPE	52	59	138	103	112	41

Figure S47. Get High-res Image Gene #5: 'amp_3q26.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_4q13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S48. Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 6(4Q13.3) MUTATED	4	3	32	19	3	18	4	3
AMP PEAK 6(4Q13.3) WILD-TYPE	17	33	87	77	106	54	16	37

Figure S48. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_4q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S49. Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 6(4Q13.3) MUTATED	22	12	31	19	2
AMP PEAK 6(4Q13.3) WILD-TYPE	79	140	83	69	56

Figure S49. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_4q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 6(4Q13.3) MUTATED	19	71	2	60	7
AMP PEAK 6(4Q13.3) WILD-TYPE	380	169	97	204	35

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

'amp_4q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S51. Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 6(4Q13.3) MUTATED	32	15	37	5	11
AMP PEAK 6(4Q13.3) WILD-TYPE	100	182	140	83	117

Figure S51. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S52. Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 6(4Q13.3) MUTATED	40	7	13	35	58	2	4
AMP PEAK 6(4Q13.3) WILD-TYPE	150	136	221	126	186	50	12

Figure S52. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_4q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S53. Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 6(4Q13.3) MUTATED	39	17	8	36	41	18
AMP PEAK 6(4Q13.3) WILD-TYPE	139	226	189	144	143	40

Figure S53. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S54. Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 6(4Q13.3) MUTATED	24	64	69
AMP PEAK 6(4Q13.3) WILD-TYPE	282	358	228

Figure S54. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_4q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S55. Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 6(4Q13.3) MUTATED	6	22	63	30	36
AMP PEAK 6(4Q13.3) WILD-TYPE	168	164	342	104	90

Figure S55. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.014

Table S56. Gene #6: 'amp_4q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 6(4Q13.3) MUTATED	38	19	47
AMP PEAK 6(4Q13.3) WILD-TYPE	211	237	162

Figure S56. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_4q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S57. Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 6(4Q13.3) MUTATED	29	3	27	21	5	19
AMP PEAK 6(4Q13.3) WILD-TYPE	98	64	166	114	120	48

Figure S57. Get High-res Image Gene #6: 'amp_4q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_5p15.33' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.14

Table S58. Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S58. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_5p15.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S59. Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 7(5P15.33) MUTATED	64	116	52	136	14
AMP PEAK 7(5P15.33) WILD-TYPE	335	124	47	128	28

Figure S59. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_5p15.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S60. Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S60. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_5p15.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 7(5P15.33) MUTATED	94	35	73	68	89	11	9
AMP PEAK 7(5P15.33) WILD-TYPE	96	108	161	93	155	41	7

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

'amp_5p15.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S62. Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 7(5P15.33) MUTATED	88	65	46	84	70	26
AMP PEAK 7(5P15.33) WILD-TYPE	90	178	151	96	114	32

Figure S62. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S63. Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 7(5P15.33) MUTATED	83	153	136
AMP PEAK 7(5P15.33) WILD-TYPE	223	269	161

Figure S63. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_5p15.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S64. Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 7(5P15.33) MUTATED	37	59	152	64	60
AMP PEAK 7(5P15.33) WILD-TYPE	137	127	253	70	66

Figure S64. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S65. Gene #7: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 7(5P15.33) MUTATED	94	67	96
AMP PEAK 7(5P15.33) WILD-TYPE	155	189	113

Figure S65. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_5p15.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S66. Gene #7: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 7(5P15.33) MUTATED	60	15	83	44	26	29
AMP PEAK 7(5P15.33) WILD-TYPE	67	52	110	91	99	38

Figure S66. Get High-res Image Gene #7: 'amp_5p15.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S67. Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S67. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S68. Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S68. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S69. Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 8(6P23) MUTATED	26	80	23	146	13
AMP PEAK 8(6P23) WILD-TYPE	373	160	76	118	29

Figure S69. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S70. Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S70. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6p23' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S71. Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S71. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6p23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S72. Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S72. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S73. Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 8(6P23) MUTATED	102	17	33	53	65	8	9
AMP PEAK 8(6P23) WILD-TYPE	88	126	201	108	179	44	7

Figure S73. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 8(6P23) MUTATED	93	38	18	78	42	18
AMP PEAK 8(6P23) WILD-TYPE	85	205	179	102	142	40

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

'amp_6p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S75. Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 8(6P23) MUTATED	39	98	139
AMP PEAK 8(6P23) WILD-TYPE	267	324	158

Figure S75. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S76. Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 8(6P23) MUTATED	12	28	111	70	55
AMP PEAK 8(6P23) WILD-TYPE	162	158	294	64	71

Figure S76. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S77. Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 8(6P23) MUTATED	49	37	97
AMP PEAK 8(6P23) WILD-TYPE	200	219	112

Figure S77. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S78. Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 8(6P23) MUTATED	62	7	50	29	12	23
AMP PEAK 8(6P23) WILD-TYPE	65	60	143	106	113	44

Figure S78. Get High-res Image Gene #8: 'amp_6p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_6q21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S79. Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S79. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_6q21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S80. Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S80. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_6q21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S81. Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 9(6Q21) MUTATED	23	22	17	131	5
AMP PEAK 9(6Q21) WILD-TYPE	376	218	82	133	37

Figure S81. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_6q21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S82. Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S82. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_6q21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S83. Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S83. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_6q21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S84. Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S84. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_6q21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S85. Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 9(6Q21) MUTATED	88	9	20	44	26	4	6
AMP PEAK 9(6Q21) WILD-TYPE	102	134	214	117	218	48	10

Figure S85. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_6q21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S86. Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 9(6Q21) MUTATED	81	13	10	53	21	19
AMP PEAK 9(6Q21) WILD-TYPE	97	230	187	127	163	39

Figure S86. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S87. Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 9(6Q21) MUTATED	19	50	119
AMP PEAK 9(6Q21) WILD-TYPE	287	372	178

Figure S87. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_6q21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S88. Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 9(6Q21) MUTATED	8	7	63	58	52
AMP PEAK 9(6Q21) WILD-TYPE	166	179	342	76	74

Figure S88. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_6q21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S89. Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 9(6Q21) MUTATED	29	16	86
AMP PEAK 9(6Q21) WILD-TYPE	220	240	123

Figure S89. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_6q21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S90. Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 9(6Q21) MUTATED	58	2	30	10	6	25
AMP PEAK 9(6Q21) WILD-TYPE	69	65	163	125	119	42

Figure S90. Get High-res Image Gene #9: 'amp_6q21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S91. Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S91. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8p11.23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S92. Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S92. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8p11.23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S93. Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 10(8P11.23) MUTATED	110	129	41	78	41
AMP PEAK 10(8P11.23) WILD-TYPE	289	111	58	186	1

Figure S93. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.23' versus 'METHLYATION_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.029

Table S94. Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S94. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.23' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S95. Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S95. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8p11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S96. Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 10(8P11.23) MUTATED	62	51	71	44	149	13	6
AMP PEAK 10(8P11.23) WILD-TYPE	128	92	163	117	95	39	10

Figure S96. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S97. Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 10(8P11.23) MUTATED	57	81	51	77	116	14
AMP PEAK 10(8P11.23) WILD-TYPE	121	162	146	103	68	44

Figure S97. Get High-res Image Gene #10: 'amp_8p11.23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S98. Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 11(8P11.21) MUTATED	103	115	44	107	42
AMP PEAK 11(8P11.21) WILD-TYPE	296	125	55	157	0

Figure S98. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8p11.21' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.018

Table S99. Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S99. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S100. Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 11(8P11.21) MUTATED	97	42	76	46	130	11	6
AMP PEAK 11(8P11.21) WILD-TYPE	93	101	158	115	114	41	10

Figure S100. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S101. Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 11(8P11.21) MUTATED	91	70	55	74	102	16
AMP PEAK 11(8P11.21) WILD-TYPE	87	173	142	106	82	42

Figure S101. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S102. Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 11(8P11.21) MUTATED	51	75	159	72	45
AMP PEAK 11(8P11.21) WILD-TYPE	123	111	246	62	81

Figure S102. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.23

Table S103. Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 11(8P11.21) MUTATED	82	84	99
AMP PEAK 11(8P11.21) WILD-TYPE	167	172	110

Figure S103. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0083

Table S104. Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 11(8P11.21) MUTATED	64	15	66	63	31	26
AMP PEAK 11(8P11.21) WILD-TYPE	63	52	127	72	94	41

Figure S104. Get High-res Image Gene #11: 'amp_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S105. Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S105. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_8q24.21' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S106. Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S106. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_8q24.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S107. Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 12(8Q24.21) MUTATED	144	191	48	239	41
AMP PEAK 12(8Q24.21) WILD-TYPE	255	49	51	25	1

Figure S107. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #3: 'CN_CNMF'

'amp_8q24.21' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S108. Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S108. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_8q24.21' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S109. Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S109. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_8q24.21' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S110. Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S110. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_8q24.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S111. Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 12(8Q24.21) MUTATED	169	66	94	114	184	19	13
AMP PEAK 12(8Q24.21) WILD-TYPE	21	77	140	47	60	33	3

Figure S111. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_8q24.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S112. Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 12(8Q24.21) MUTATED	159	108	72	139	138	43
AMP PEAK 12(8Q24.21) WILD-TYPE	19	135	125	41	46	15

Figure S112. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S113. Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 12(8Q24.21) MUTATED	134	255	259
AMP PEAK 12(8Q24.21) WILD-TYPE	172	167	38

Figure S113. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_8q24.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S114. Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 12(8Q24.21) MUTATED	59	95	268	123	103
AMP PEAK 12(8Q24.21) WILD-TYPE	115	91	137	11	23

Figure S114. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S115. Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 12(8Q24.21) MUTATED	139	109	184
AMP PEAK 12(8Q24.21) WILD-TYPE	110	147	25

Figure S115. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_8q24.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S116. Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 12(8Q24.21) MUTATED	113	23	122	79	39	56
AMP PEAK 12(8Q24.21) WILD-TYPE	14	44	71	56	86	11

Figure S116. Get High-res Image Gene #12: 'amp_8q24.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

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

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

'amp_10p15.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S118. Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S118. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10p15.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S119. Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 13(10P15.1) MUTATED	33	67	19	166	9
AMP PEAK 13(10P15.1) WILD-TYPE	366	173	80	98	33

Figure S119. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_10p15.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S120. Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S120. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_10p15.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S121. Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S121. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_10p15.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S122. Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S122. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_10p15.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S123. Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 13(10P15.1) MUTATED	122	17	26	58	56	8	7
AMP PEAK 13(10P15.1) WILD-TYPE	68	126	208	103	188	44	9

Figure S123. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10p15.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S124. Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 13(10P15.1) MUTATED	121	29	14	64	41	25
AMP PEAK 13(10P15.1) WILD-TYPE	57	214	183	116	143	33

Figure S124. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S125. Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 13(10P15.1) MUTATED	42	80	164
AMP PEAK 13(10P15.1) WILD-TYPE	264	342	133

Figure S125. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10p15.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S126. Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 13(10P15.1) MUTATED	11	20	101	90	64
AMP PEAK 13(10P15.1) WILD-TYPE	163	166	304	44	62

Figure S126. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S127. Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 13(10P15.1) MUTATED	45	34	111
AMP PEAK 13(10P15.1) WILD-TYPE	204	222	98

Figure S127. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10p15.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S128. Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 13(10P15.1) MUTATED	81	7	39	24	10	29
AMP PEAK 13(10P15.1) WILD-TYPE	46	60	154	111	115	38

Figure S128. Get High-res Image Gene #13: 'amp_10p15.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_10q22.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S129. Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S129. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_10q22.3' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.02

Table S130. Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S130. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_10q22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 14(10Q22.3) MUTATED	21	39	15	65	6
AMP PEAK 14(10Q22.3) WILD-TYPE	378	201	84	199	36

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

'amp_10q22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S132. Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 14(10Q22.3) MUTATED	33	10	20	41	30	4	8
AMP PEAK 14(10Q22.3) WILD-TYPE	157	133	214	120	214	48	8

Figure S132. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_10q22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S133. Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 14(10Q22.3) MUTATED	30	15	13	46	26	16
AMP PEAK 14(10Q22.3) WILD-TYPE	148	228	184	134	158	42

Figure S133. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.06

Table S134. Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 14(10Q22.3) MUTATED	26	57	59
AMP PEAK 14(10Q22.3) WILD-TYPE	280	365	238

Figure S134. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_10q22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S135. Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 14(10Q22.3) MUTATED	9	12	70	23	28
AMP PEAK 14(10Q22.3) WILD-TYPE	165	174	335	111	98

Figure S135. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.084

Table S136. Gene #14: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 14(10Q22.3) MUTATED	36	18	40
AMP PEAK 14(10Q22.3) WILD-TYPE	213	238	169

Figure S136. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_10q22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S137. Gene #14: 'amp_10q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 14(10Q22.3) MUTATED	19	4	34	12	6	19
AMP PEAK 14(10Q22.3) WILD-TYPE	108	63	159	123	119	48

Figure S137. Get High-res Image Gene #14: 'amp_10q22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11p13' versus 'MRNA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.16

Table S138. Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S138. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S139. Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 15(11P13) MUTATED	32	73	17	87	8
AMP PEAK 15(11P13) WILD-TYPE	367	167	82	177	34

Figure S139. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S140. Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 15(11P13) MUTATED	61	13	27	38	66	9	3
AMP PEAK 15(11P13) WILD-TYPE	129	130	207	123	178	43	13

Figure S140. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S141. Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 15(11P13) MUTATED	59	35	14	51	49	9
AMP PEAK 15(11P13) WILD-TYPE	119	208	183	129	135	49

Figure S141. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S142. Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 15(11P13) MUTATED	32	88	94
AMP PEAK 15(11P13) WILD-TYPE	274	334	203

Figure S142. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S143. Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 15(11P13) MUTATED	10	31	92	39	42
AMP PEAK 15(11P13) WILD-TYPE	164	155	313	95	84

Figure S143. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S144. Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 15(11P13) MUTATED	50	25	61
AMP PEAK 15(11P13) WILD-TYPE	199	231	148

Figure S144. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S145. Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 15(11P13) MUTATED	41	5	49	21	8	12
AMP PEAK 15(11P13) WILD-TYPE	86	62	144	114	117	55

Figure S145. Get High-res Image Gene #15: 'amp_11p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S146. Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S146. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_11q13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S147. Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S147. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S148. Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 16(11Q13.3) MUTATED	69	174	28	100	15
AMP PEAK 16(11Q13.3) WILD-TYPE	330	66	71	164	27

Figure S148. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S149. Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S149. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q13.3' versus 'RPPA_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.11

Table S150. Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S150. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_11q13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S151. Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 16(11Q13.3) MUTATED	61	40	55	69	136	16	9
AMP PEAK 16(11Q13.3) WILD-TYPE	129	103	179	92	108	36	7

Figure S151. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S152. Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 16(11Q13.3) MUTATED	58	71	36	93	108	20
AMP PEAK 16(11Q13.3) WILD-TYPE	120	172	161	87	76	38

Figure S152. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.099

Table S153. Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 16(11Q13.3) MUTATED	86	176	116
AMP PEAK 16(11Q13.3) WILD-TYPE	220	246	181

Figure S153. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S154. Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 16(11Q13.3) MUTATED	36	71	178	43	50
AMP PEAK 16(11Q13.3) WILD-TYPE	138	115	227	91	76

Figure S154. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.055

Table S155. Gene #16: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 16(11Q13.3) MUTATED	48	13	76	59	28	24
AMP PEAK 16(11Q13.3) WILD-TYPE	79	54	117	76	97	43

Figure S155. Get High-res Image Gene #16: 'amp_11q13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_11q14.1' versus 'MRNA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.02

Table S156. Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S156. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_11q14.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S157. Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 17(11Q14.1) MUTATED	40	94	18	97	9
AMP PEAK 17(11Q14.1) WILD-TYPE	359	146	81	167	33

Figure S157. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_11q14.1' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.02

Table S158. Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S158. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S159. Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 17(11Q14.1) MUTATED	64	24	34	49	75	7	5
AMP PEAK 17(11Q14.1) WILD-TYPE	126	119	200	112	169	45	11

Figure S159. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_11q14.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S160. Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 17(11Q14.1) MUTATED	61	38	25	63	54	17
AMP PEAK 17(11Q14.1) WILD-TYPE	117	205	172	117	130	41

Figure S160. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S161. Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 17(11Q14.1) MUTATED	45	104	103
AMP PEAK 17(11Q14.1) WILD-TYPE	261	318	194

Figure S161. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_11q14.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.018

Table S162. Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 17(11Q14.1) MUTATED	21	43	104	47	37
AMP PEAK 17(11Q14.1) WILD-TYPE	153	143	301	87	89

Figure S162. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S163. Gene #17: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 17(11Q14.1) MUTATED	55	38	70
AMP PEAK 17(11Q14.1) WILD-TYPE	194	218	139

Figure S163. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_11q14.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S164. Gene #17: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 17(11Q14.1) MUTATED	44	10	51	28	12	18
AMP PEAK 17(11Q14.1) WILD-TYPE	83	57	142	107	113	49

Figure S164. Get High-res Image Gene #17: 'amp_11q14.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S165. Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S165. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12p13.33' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S166. Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S166. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12p13.33' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S167. Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 18(12P13.33) MUTATED	19	83	29	135	11
AMP PEAK 18(12P13.33) WILD-TYPE	380	157	70	129	31

Figure S167. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12p13.33' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S168. Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S168. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12p13.33' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S169. Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S169. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_12p13.33' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S170. Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S170. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_12p13.33' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S171. Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 18(12P13.33) MUTATED	107	13	32	49	69	4	3
AMP PEAK 18(12P13.33) WILD-TYPE	83	130	202	112	175	48	13

Figure S171. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12p13.33' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S172. Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 18(12P13.33) MUTATED	101	29	22	60	51	14
AMP PEAK 18(12P13.33) WILD-TYPE	77	214	175	120	133	44

Figure S172. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S173. Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 18(12P13.33) MUTATED	41	87	140
AMP PEAK 18(12P13.33) WILD-TYPE	265	335	157

Figure S173. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12p13.33' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S174. Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 18(12P13.33) MUTATED	14	28	104	76	46
AMP PEAK 18(12P13.33) WILD-TYPE	160	158	301	58	80

Figure S174. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S175. Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 18(12P13.33) MUTATED	41	35	101
AMP PEAK 18(12P13.33) WILD-TYPE	208	221	108

Figure S175. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_12p13.33' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S176. Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 18(12P13.33) MUTATED	71	6	43	27	11	19
AMP PEAK 18(12P13.33) WILD-TYPE	56	61	150	108	114	48

Figure S176. Get High-res Image Gene #18: 'amp_12p13.33' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_12q15' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S177. Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S177. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_12q15' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S178. Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S178. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_12q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S179. Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 19(12Q15) MUTATED	29	130	32	68	10
AMP PEAK 19(12Q15) WILD-TYPE	370	110	67	196	32

Figure S179. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #3: 'CN_CNMF'

'amp_12q15' versus 'METHLYATION_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S180. Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S180. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_12q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S181. Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 19(12Q15) MUTATED	31	17	42	61	102	11	4
AMP PEAK 19(12Q15) WILD-TYPE	159	126	192	100	142	41	12

Figure S181. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_12q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S182. Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 19(12Q15) MUTATED	29	40	28	85	74	12
AMP PEAK 19(12Q15) WILD-TYPE	149	203	169	95	110	46

Figure S182. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S183. Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 19(12Q15) MUTATED	52	134	77
AMP PEAK 19(12Q15) WILD-TYPE	254	288	220

Figure S183. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_12q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S184. Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 19(12Q15) MUTATED	20	44	141	21	37
AMP PEAK 19(12Q15) WILD-TYPE	154	142	264	113	89

Figure S184. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_12q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S185. Gene #19: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 19(12Q15) MUTATED	17	7	69	39	16	17
AMP PEAK 19(12Q15) WILD-TYPE	110	60	124	96	109	50

Figure S185. Get High-res Image Gene #19: 'amp_12q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_13q34' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S186. Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S186. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_13q34' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S187. Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S187. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_13q34' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S188. Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 20(13Q34) MUTATED	25	39	12	94	6
AMP PEAK 20(13Q34) WILD-TYPE	374	201	87	170	36

Figure S188. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #3: 'CN_CNMF'

'amp_13q34' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S189. Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S189. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_13q34' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S190. Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

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

Figure S190. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_13q34' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S191. Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

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

Figure S191. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_13q34' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S192. Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 20(13Q34) MUTATED	77	9	23	26	34	4	3
AMP PEAK 20(13Q34) WILD-TYPE	113	134	211	135	210	48	13

Figure S192. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_13q34' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S193. Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 20(13Q34) MUTATED	72	15	18	28	27	16
AMP PEAK 20(13Q34) WILD-TYPE	106	228	179	152	157	42

Figure S193. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S194. Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 20(13Q34) MUTATED	28	43	102
AMP PEAK 20(13Q34) WILD-TYPE	278	379	195

Figure S194. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_13q34' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S195. Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 20(13Q34) MUTATED	9	14	58	54	38
AMP PEAK 20(13Q34) WILD-TYPE	165	172	347	80	88

Figure S195. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_13q34' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S196. Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 20(13Q34) MUTATED	24	21	62
AMP PEAK 20(13Q34) WILD-TYPE	225	235	147

Figure S196. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_13q34' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S197. Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 20(13Q34) MUTATED	44	2	20	20	6	15
AMP PEAK 20(13Q34) WILD-TYPE	83	65	173	115	119	52

Figure S197. Get High-res Image Gene #20: 'amp_13q34' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_14q21.1' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S198. Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S198. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_14q21.1' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S199. Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S199. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_14q21.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S200. Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 21(14Q21.1) MUTATED	34	92	25	52	10
AMP PEAK 21(14Q21.1) WILD-TYPE	365	148	74	212	32

Figure S200. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_14q21.1' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S201. Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S201. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S202. Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 21(14Q21.1) MUTATED	21	17	43	51	72	3	4
AMP PEAK 21(14Q21.1) WILD-TYPE	169	126	191	110	172	49	12

Figure S202. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_14q21.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S203. Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 21(14Q21.1) MUTATED	17	27	31	73	46	17
AMP PEAK 21(14Q21.1) WILD-TYPE	161	216	166	107	138	41

Figure S203. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.016

Table S204. Gene #21: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 21(14Q21.1) MUTATED	39	110	58
AMP PEAK 21(14Q21.1) WILD-TYPE	267	312	239

Figure S204. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_14q21.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S205. Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 21(14Q21.1) MUTATED	16	22	122	11	36
AMP PEAK 21(14Q21.1) WILD-TYPE	158	164	283	123	90

Figure S205. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_14q21.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S206. Gene #21: 'amp_14q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 21(14Q21.1) MUTATED	14	5	61	32	11	19
AMP PEAK 21(14Q21.1) WILD-TYPE	113	62	132	103	114	48

Figure S206. Get High-res Image Gene #21: 'amp_14q21.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_15q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S207. Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

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

Figure S207. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_15q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.031

Table S208. Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

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

Figure S208. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_15q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S209. Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 22(15Q26.3) MUTATED	28	59	8	90	2
AMP PEAK 22(15Q26.3) WILD-TYPE	371	181	91	174	40

Figure S209. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'amp_15q26.3' versus 'METHLYATION_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.19

Table S210. Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

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

Figure S210. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S211. Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 22(15Q26.3) MUTATED	63	15	19	27	56	3	3
AMP PEAK 22(15Q26.3) WILD-TYPE	127	128	215	134	188	49	13

Figure S211. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_15q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S212. Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 22(15Q26.3) MUTATED	60	21	18	34	46	7
AMP PEAK 22(15Q26.3) WILD-TYPE	118	222	179	146	138	51

Figure S212. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S213. Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 22(15Q26.3) MUTATED	33	64	83
AMP PEAK 22(15Q26.3) WILD-TYPE	273	358	214

Figure S213. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_15q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S214. Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 22(15Q26.3) MUTATED	8	21	71	44	36
AMP PEAK 22(15Q26.3) WILD-TYPE	166	165	334	90	90

Figure S214. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.031

Table S215. Gene #22: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 22(15Q26.3) MUTATED	41	28	54
AMP PEAK 22(15Q26.3) WILD-TYPE	208	228	155

Figure S215. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_15q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S216. Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 22(15Q26.3) MUTATED	39	6	38	20	8	12
AMP PEAK 22(15Q26.3) WILD-TYPE	88	61	155	115	117	55

Figure S216. Get High-res Image Gene #22: 'amp_15q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S217. Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 23(17Q12) MUTATED	9	11	53	19	14	49	7	4
AMP PEAK 23(17Q12) WILD-TYPE	12	25	66	77	95	23	13	36

Figure S217. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S218. Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 23(17Q12) MUTATED	40	28	71	16	11
AMP PEAK 23(17Q12) WILD-TYPE	61	124	43	72	47

Figure S218. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S219. Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 23(17Q12) MUTATED	59	159	25	64	13
AMP PEAK 23(17Q12) WILD-TYPE	340	81	74	200	29

Figure S219. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S220. Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 23(17Q12) MUTATED	33	46	85	23	29
AMP PEAK 23(17Q12) WILD-TYPE	99	151	92	65	99

Figure S220. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S221. Gene #23: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 23(17Q12) MUTATED	9	28	20	41	31
AMP PEAK 23(17Q12) WILD-TYPE	55	78	70	66	0

Figure S221. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S222. Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 23(17Q12) MUTATED	35	28	37	101	108	6	4
AMP PEAK 23(17Q12) WILD-TYPE	155	115	197	60	136	46	12

Figure S222. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S223. Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 23(17Q12) MUTATED	31	44	28	91	88	37
AMP PEAK 23(17Q12) WILD-TYPE	147	199	169	89	96	21

Figure S223. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_CNMF'

P value = 0.00118 (Fisher's exact test), Q value = 0.2

Table S224. Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 23(17Q12) MUTATED	70	148	95
AMP PEAK 23(17Q12) WILD-TYPE	236	274	202

Figure S224. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S225. Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 23(17Q12) MUTATED	25	52	164	20	52
AMP PEAK 23(17Q12) WILD-TYPE	149	134	241	114	74

Figure S225. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S226. Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 23(17Q12) MUTATED	24	14	70	53	16	41
AMP PEAK 23(17Q12) WILD-TYPE	103	53	123	82	109	26

Figure S226. Get High-res Image Gene #23: 'amp_17q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S227. Gene #24: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 24(17Q23.1) MUTATED	9	17	81	29	16	44	11	9
AMP PEAK 24(17Q23.1) WILD-TYPE	12	19	38	67	93	28	9	31

Figure S227. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_17q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S228. Gene #24: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 24(17Q23.1) MUTATED	62	45	71	25	13
AMP PEAK 24(17Q23.1) WILD-TYPE	39	107	43	63	45

Figure S228. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_17q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S229. Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 24(17Q23.1) MUTATED	69	189	28	113	18
AMP PEAK 24(17Q23.1) WILD-TYPE	330	51	71	151	24

Figure S229. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'amp_17q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S230. Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 24(17Q23.1) MUTATED	52	61	99	28	40
AMP PEAK 24(17Q23.1) WILD-TYPE	80	136	78	60	88

Figure S230. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_17q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S231. Gene #24: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 24(17Q23.1) MUTATED	13	40	26	68	19
AMP PEAK 24(17Q23.1) WILD-TYPE	51	66	64	39	12

Figure S231. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_17q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S232. Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 24(17Q23.1) MUTATED	66	40	40	91	156	14	9
AMP PEAK 24(17Q23.1) WILD-TYPE	124	103	194	70	88	38	7

Figure S232. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_17q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S233. Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 24(17Q23.1) MUTATED	59	68	32	111	117	29
AMP PEAK 24(17Q23.1) WILD-TYPE	119	175	165	69	67	29

Figure S233. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S234. Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 24(17Q23.1) MUTATED	80	187	142
AMP PEAK 24(17Q23.1) WILD-TYPE	226	235	155

Figure S234. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_17q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S235. Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 24(17Q23.1) MUTATED	33	71	197	43	65
AMP PEAK 24(17Q23.1) WILD-TYPE	141	115	208	91	61

Figure S235. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.016

Table S236. Gene #24: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 24(17Q23.1) MUTATED	97	74	102
AMP PEAK 24(17Q23.1) WILD-TYPE	152	182	107

Figure S236. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_17q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S237. Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 24(17Q23.1) MUTATED	46	19	83	63	23	39
AMP PEAK 24(17Q23.1) WILD-TYPE	81	48	110	72	102	28

Figure S237. Get High-res Image Gene #24: 'amp_17q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19p13.12' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.018

Table S238. Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 25(19P13.12) MUTATED	5	6	22	40	16	11	5	4
AMP PEAK 25(19P13.12) WILD-TYPE	16	30	97	56	93	61	15	36

Figure S238. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19p13.12' versus 'MRNA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.052

Table S239. Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 25(19P13.12) MUTATED	19	21	23	35	11
AMP PEAK 25(19P13.12) WILD-TYPE	82	131	91	53	47

Figure S239. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19p13.12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S240. Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 25(19P13.12) MUTATED	36	47	30	98	10
AMP PEAK 25(19P13.12) WILD-TYPE	363	193	69	166	32

Figure S240. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19p13.12' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S241. Gene #25: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 25(19P13.12) MUTATED	47	25	31	16	26
AMP PEAK 25(19P13.12) WILD-TYPE	85	172	146	72	102

Figure S241. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19p13.12' versus 'RPPA_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.15

Table S242. Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 25(19P13.12) MUTATED	49	25	17
AMP PEAK 25(19P13.12) WILD-TYPE	100	107	100

Figure S242. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S243. Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 25(19P13.12) MUTATED	78	27	29	32	42	6	5
AMP PEAK 25(19P13.12) WILD-TYPE	112	116	205	129	202	46	11

Figure S243. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19p13.12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S244. Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 25(19P13.12) MUTATED	72	41	22	35	36	13
AMP PEAK 25(19P13.12) WILD-TYPE	106	202	175	145	148	45

Figure S244. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S245. Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 25(19P13.12) MUTATED	55	60	100
AMP PEAK 25(19P13.12) WILD-TYPE	251	362	197

Figure S245. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19p13.12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S246. Gene #25: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 25(19P13.12) MUTATED	27	23	73	56	36
AMP PEAK 25(19P13.12) WILD-TYPE	147	163	332	78	90

Figure S246. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S247. Gene #25: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 25(19P13.12) MUTATED	41	46	68
AMP PEAK 25(19P13.12) WILD-TYPE	208	210	141

Figure S247. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19p13.12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0083

Table S248. Gene #25: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 25(19P13.12) MUTATED	49	13	33	25	17	18
AMP PEAK 25(19P13.12) WILD-TYPE	78	54	160	110	108	49

Figure S248. Get High-res Image Gene #25: 'amp_19p13.12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S249. Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 26(19Q12) MUTATED	4	5	29	55	15	20	7	5
AMP PEAK 26(19Q12) WILD-TYPE	17	31	90	41	94	52	13	35

Figure S249. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S250. Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 26(19Q12) MUTATED	20	24	35	50	11
AMP PEAK 26(19Q12) WILD-TYPE	81	128	79	38	47

Figure S250. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_19q12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S251. Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 26(19Q12) MUTATED	36	54	32	138	13
AMP PEAK 26(19Q12) WILD-TYPE	363	186	67	126	29

Figure S251. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S252. Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 26(19Q12) MUTATED	69	29	43	15	25
AMP PEAK 26(19Q12) WILD-TYPE	63	168	134	73	103

Figure S252. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S253. Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 26(19Q12) MUTATED	64	22	24
AMP PEAK 26(19Q12) WILD-TYPE	85	110	93

Figure S253. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S254. Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 26(19Q12) MUTATED	15	21	46	18	10
AMP PEAK 26(19Q12) WILD-TYPE	49	85	44	89	21

Figure S254. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_19q12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S255. Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 26(19Q12) MUTATED	106	24	31	48	52	5	6
AMP PEAK 26(19Q12) WILD-TYPE	84	119	203	113	192	47	10

Figure S255. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S256. Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 26(19Q12) MUTATED	101	40	22	45	41	23
AMP PEAK 26(19Q12) WILD-TYPE	77	203	175	135	143	35

Figure S256. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S257. Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 26(19Q12) MUTATED	51	78	140
AMP PEAK 26(19Q12) WILD-TYPE	255	344	157

Figure S257. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S258. Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 26(19Q12) MUTATED	24	26	91	75	53
AMP PEAK 26(19Q12) WILD-TYPE	150	160	314	59	73

Figure S258. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_19q12' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S259. Gene #26: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 26(19Q12) MUTATED	46	48	97
AMP PEAK 26(19Q12) WILD-TYPE	203	208	112

Figure S259. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_19q12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S260. Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 26(19Q12) MUTATED	70	12	44	30	14	21
AMP PEAK 26(19Q12) WILD-TYPE	57	55	149	105	111	46

Figure S260. Get High-res Image Gene #26: 'amp_19q12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_19q13.42' versus 'MRNA_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.082

Table S261. Gene #27: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 27(19Q13.42) MUTATED	5	8	36	40	17	20	10	6
AMP PEAK 27(19Q13.42) WILD-TYPE	16	28	83	56	92	52	10	34

Figure S261. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_19q13.42' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S262. Gene #27: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 27(19Q13.42) MUTATED	39	72	34	106	17
AMP PEAK 27(19Q13.42) WILD-TYPE	360	168	65	158	25

Figure S262. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #3: 'CN_CNMF'

'amp_19q13.42' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.16

Table S263. Gene #27: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 27(19Q13.42) MUTATED	42	35	56	19	21
AMP PEAK 27(19Q13.42) WILD-TYPE	90	162	121	69	107

Figure S263. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_19q13.42' versus 'RPPA_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.2

Table S264. Gene #27: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 27(19Q13.42) MUTATED	57	26	27
AMP PEAK 27(19Q13.42) WILD-TYPE	92	106	90

Figure S264. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S265. Gene #27: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 27(19Q13.42) MUTATED	67	29	34	48	74	6	9
AMP PEAK 27(19Q13.42) WILD-TYPE	123	114	200	113	170	46	7

Figure S265. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_19q13.42' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S266. Gene #27: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 27(19Q13.42) MUTATED	61	47	25	58	58	18
AMP PEAK 27(19Q13.42) WILD-TYPE	117	196	172	122	126	40

Figure S266. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_19q13.42' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.023

Table S267. Gene #27: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 27(19Q13.42) MUTATED	62	99	103
AMP PEAK 27(19Q13.42) WILD-TYPE	244	323	194

Figure S267. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_19q13.42' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S268. Gene #27: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 27(19Q13.42) MUTATED	28	36	109	44	47
AMP PEAK 27(19Q13.42) WILD-TYPE	146	150	296	90	79

Figure S268. Get High-res Image Gene #27: 'amp_19q13.42' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S269. Gene #28: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
AMP PEAK 28(20Q13.2) MUTATED	12	18	85	52	35	49	15	10
AMP PEAK 28(20Q13.2) WILD-TYPE	9	18	34	44	74	23	5	30

Figure S269. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'amp_20q13.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S270. Gene #28: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
AMP PEAK 28(20Q13.2) MUTATED	73	56	86	44	17
AMP PEAK 28(20Q13.2) WILD-TYPE	28	96	28	44	41

Figure S270. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'amp_20q13.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S271. Gene #28: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
AMP PEAK 28(20Q13.2) MUTATED	78	197	60	175	25
AMP PEAK 28(20Q13.2) WILD-TYPE	321	43	39	89	17

Figure S271. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #3: 'CN_CNMF'

'amp_20q13.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S272. Gene #28: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
AMP PEAK 28(20Q13.2) MUTATED	83	78	113	29	49
AMP PEAK 28(20Q13.2) WILD-TYPE	49	119	64	59	79

Figure S272. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'amp_20q13.2' versus 'RPPA_CNMF'

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

Table S273. Gene #28: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
AMP PEAK 28(20Q13.2) MUTATED	101	66	54
AMP PEAK 28(20Q13.2) WILD-TYPE	48	66	63

Figure S273. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'amp_20q13.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.053

Table S274. Gene #28: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
AMP PEAK 28(20Q13.2) MUTATED	29	44	53	73	22
AMP PEAK 28(20Q13.2) WILD-TYPE	35	62	37	34	9

Figure S274. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'amp_20q13.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S275. Gene #28: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
AMP PEAK 28(20Q13.2) MUTATED	104	45	79	106	170	18	10
AMP PEAK 28(20Q13.2) WILD-TYPE	86	98	155	55	74	34	6

Figure S275. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'amp_20q13.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S276. Gene #28: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
AMP PEAK 28(20Q13.2) MUTATED	96	86	52	130	135	33
AMP PEAK 28(20Q13.2) WILD-TYPE	82	157	145	50	49	25

Figure S276. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S277. Gene #28: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
AMP PEAK 28(20Q13.2) MUTATED	113	233	181
AMP PEAK 28(20Q13.2) WILD-TYPE	193	189	116

Figure S277. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'amp_20q13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S278. Gene #28: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
AMP PEAK 28(20Q13.2) MUTATED	49	80	248	71	79
AMP PEAK 28(20Q13.2) WILD-TYPE	125	106	157	63	47

Figure S278. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S279. Gene #28: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
AMP PEAK 28(20Q13.2) MUTATED	140	95	129
AMP PEAK 28(20Q13.2) WILD-TYPE	109	161	80

Figure S279. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'amp_20q13.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S280. Gene #28: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
AMP PEAK 28(20Q13.2) MUTATED	72	22	123	69	36	42
AMP PEAK 28(20Q13.2) WILD-TYPE	55	45	70	66	89	25

Figure S280. Get High-res Image Gene #28: 'amp_20q13.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_1p36.13' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.016

Table S281. Gene #29: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 1(1P36.13) MUTATED	9	11	61	42	31	46	7	12
DEL PEAK 1(1P36.13) WILD-TYPE	12	25	58	54	78	26	13	28

Figure S281. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_1p36.13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S282. Gene #29: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 1(1P36.13) MUTATED	57	39	67	39	17
DEL PEAK 1(1P36.13) WILD-TYPE	44	113	47	49	41

Figure S282. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p36.13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S283. Gene #29: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 1(1P36.13) MUTATED	68	157	60	135	17
DEL PEAK 1(1P36.13) WILD-TYPE	331	83	39	129	25

Figure S283. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p36.13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S284. Gene #29: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 1(1P36.13) MUTATED	58	64	110	24	36
DEL PEAK 1(1P36.13) WILD-TYPE	74	133	67	64	92

Figure S284. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p36.13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S285. Gene #29: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 1(1P36.13) MUTATED	79	32	82	89	127	18	7
DEL PEAK 1(1P36.13) WILD-TYPE	111	111	152	72	117	34	9

Figure S285. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p36.13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S286. Gene #29: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 1(1P36.13) MUTATED	79	75	54	113	97	16
DEL PEAK 1(1P36.13) WILD-TYPE	99	168	143	67	87	42

Figure S286. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p36.13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S287. Gene #29: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 1(1P36.13) MUTATED	92	190	141
DEL PEAK 1(1P36.13) WILD-TYPE	214	232	156

Figure S287. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p36.13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S288. Gene #29: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 1(1P36.13) MUTATED	40	61	210	60	52
DEL PEAK 1(1P36.13) WILD-TYPE	134	125	195	74	74

Figure S288. Get High-res Image Gene #29: 'del_1p36.13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_1p21.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S289. Gene #30: 'del_1p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 2(1P21.2) MUTATED	47	37	60	20	15
DEL PEAK 2(1P21.2) WILD-TYPE	54	115	54	68	43

Figure S289. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_1p21.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S290. Gene #30: 'del_1p21.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 2(1P21.2) MUTATED	62	129	57	84	13
DEL PEAK 2(1P21.2) WILD-TYPE	337	111	42	180	29

Figure S290. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_1p21.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S291. Gene #30: 'del_1p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 2(1P21.2) MUTATED	36	54	86	22	26
DEL PEAK 2(1P21.2) WILD-TYPE	96	143	91	66	102

Figure S291. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_1p21.2' versus 'RPPA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.06

Table S292. Gene #30: 'del_1p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 2(1P21.2) MUTATED	61	50	23
DEL PEAK 2(1P21.2) WILD-TYPE	88	82	94

Figure S292. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_1p21.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S293. Gene #30: 'del_1p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 2(1P21.2) MUTATED	43	30	75	79	103	9	4
DEL PEAK 2(1P21.2) WILD-TYPE	147	113	159	82	141	43	12

Figure S293. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_1p21.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S294. Gene #30: 'del_1p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 2(1P21.2) MUTATED	39	67	47	101	74	15
DEL PEAK 2(1P21.2) WILD-TYPE	139	176	150	79	110	43

Figure S294. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_1p21.2' versus 'MIRSEQ_CNMF'

P value = 0.00149 (Fisher's exact test), Q value = 0.24

Table S295. Gene #30: 'del_1p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 2(1P21.2) MUTATED	81	164	93
DEL PEAK 2(1P21.2) WILD-TYPE	225	258	204

Figure S295. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_1p21.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S296. Gene #30: 'del_1p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 2(1P21.2) MUTATED	39	49	180	28	42
DEL PEAK 2(1P21.2) WILD-TYPE	135	137	225	106	84

Figure S296. Get High-res Image Gene #30: 'del_1p21.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2p25.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S297. Gene #31: 'del_2p25.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 3(2P25.1) MUTATED	33	72	29	53	11
DEL PEAK 3(2P25.1) WILD-TYPE	366	168	70	211	31

Figure S297. Get High-res Image Gene #31: 'del_2p25.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_2p25.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S298. Gene #31: 'del_2p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 3(2P25.1) MUTATED	29	32	34	46	52	2
DEL PEAK 3(2P25.1) WILD-TYPE	149	211	163	134	132	56

Figure S298. Get High-res Image Gene #31: 'del_2p25.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2p25.1' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.039

Table S299. Gene #31: 'del_2p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 3(2P25.1) MUTATED	40	104	47
DEL PEAK 3(2P25.1) WILD-TYPE	266	318	250

Figure S299. Get High-res Image Gene #31: 'del_2p25.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2p25.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.02

Table S300. Gene #31: 'del_2p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 3(2P25.1) MUTATED	18	41	96	23	13
DEL PEAK 3(2P25.1) WILD-TYPE	156	145	309	111	113

Figure S300. Get High-res Image Gene #31: 'del_2p25.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S301. Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 4(2Q37.3) MUTATED	5	9	42	49	24	28	6	0
DEL PEAK 4(2Q37.3) WILD-TYPE	16	27	77	47	85	44	14	40

Figure S301. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_2q37.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S302. Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 4(2Q37.3) MUTATED	40	22	48	43	10
DEL PEAK 4(2Q37.3) WILD-TYPE	61	130	66	45	48

Figure S302. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_2q37.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S303. Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 4(2Q37.3) MUTATED	40	97	31	128	14
DEL PEAK 4(2Q37.3) WILD-TYPE	359	143	68	136	28

Figure S303. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_2q37.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S304. Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 4(2Q37.3) MUTATED	64	46	49	15	19
DEL PEAK 4(2Q37.3) WILD-TYPE	68	151	128	73	109

Figure S304. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_2q37.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S305. Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 4(2Q37.3) MUTATED	73	40	14
DEL PEAK 4(2Q37.3) WILD-TYPE	76	92	103

Figure S305. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_2q37.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S306. Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 4(2Q37.3) MUTATED	19	10	41	45	12
DEL PEAK 4(2Q37.3) WILD-TYPE	45	96	49	62	19

Figure S306. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_2q37.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S307. Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 4(2Q37.3) MUTATED	93	19	50	59	79	4	3
DEL PEAK 4(2Q37.3) WILD-TYPE	97	124	184	102	165	48	13

Figure S307. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_2q37.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S308. Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 4(2Q37.3) MUTATED	87	30	34	75	67	14
DEL PEAK 4(2Q37.3) WILD-TYPE	91	213	163	105	117	44

Figure S308. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S309. Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 4(2Q37.3) MUTATED	47	122	133
DEL PEAK 4(2Q37.3) WILD-TYPE	259	300	164

Figure S309. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_2q37.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S310. Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 4(2Q37.3) MUTATED	17	47	128	68	42
DEL PEAK 4(2Q37.3) WILD-TYPE	157	139	277	66	84

Figure S310. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_2q37.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S311. Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 4(2Q37.3) MUTATED	65	37	102
DEL PEAK 4(2Q37.3) WILD-TYPE	184	219	107

Figure S311. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_2q37.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S312. Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 4(2Q37.3) MUTATED	64	13	65	34	10	18
DEL PEAK 4(2Q37.3) WILD-TYPE	63	54	128	101	115	49

Figure S312. Get High-res Image Gene #32: 'del_2q37.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_3p21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S313. Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 5(3P21.31) MUTATED	5	15	38	52	8	35	9	7
DEL PEAK 5(3P21.31) WILD-TYPE	16	21	81	44	101	37	11	33

Figure S313. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_3p21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S314. Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 5(3P21.31) MUTATED	29	36	55	48	1
DEL PEAK 5(3P21.31) WILD-TYPE	72	116	59	40	57

Figure S314. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_3p21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S315. Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 5(3P21.31) MUTATED	56	92	20	165	4
DEL PEAK 5(3P21.31) WILD-TYPE	343	148	79	99	38

Figure S315. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_3p21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S316. Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 5(3P21.31) MUTATED	70	31	74	23	27
DEL PEAK 5(3P21.31) WILD-TYPE	62	166	103	65	101

Figure S316. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_3p21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S317. Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 5(3P21.31) MUTATED	81	27	36
DEL PEAK 5(3P21.31) WILD-TYPE	68	105	81

Figure S317. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_3p21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S318. Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 5(3P21.31) MUTATED	5	32	55	41	11
DEL PEAK 5(3P21.31) WILD-TYPE	59	74	35	66	20

Figure S318. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_3p21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S319. Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 5(3P21.31) MUTATED	103	30	27	76	81	12	7
DEL PEAK 5(3P21.31) WILD-TYPE	87	113	207	85	163	40	9

Figure S319. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_3p21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S320. Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 5(3P21.31) MUTATED	98	51	23	90	50	24
DEL PEAK 5(3P21.31) WILD-TYPE	80	192	174	90	134	34

Figure S320. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S321. Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 5(3P21.31) MUTATED	58	117	155
DEL PEAK 5(3P21.31) WILD-TYPE	248	305	142

Figure S321. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_3p21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S322. Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 5(3P21.31) MUTATED	28	35	136	74	57
DEL PEAK 5(3P21.31) WILD-TYPE	146	151	269	60	69

Figure S322. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_3p21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S323. Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 5(3P21.31) MUTATED	63	55	110
DEL PEAK 5(3P21.31) WILD-TYPE	186	201	99

Figure S323. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_3p21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S324. Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 5(3P21.31) MUTATED	68	12	63	31	23	31
DEL PEAK 5(3P21.31) WILD-TYPE	59	55	130	104	102	36

Figure S324. Get High-res Image Gene #33: 'del_3p21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4p16.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S325. Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 6(4P16.3) MUTATED	3	10	25	58	22	38	7	6
DEL PEAK 6(4P16.3) WILD-TYPE	18	26	94	38	87	34	13	34

Figure S325. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4p16.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S326. Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 6(4P16.3) MUTATED	27	28	51	52	11
DEL PEAK 6(4P16.3) WILD-TYPE	74	124	63	36	47

Figure S326. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4p16.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S327. Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 6(4P16.3) MUTATED	47	69	45	159	10
DEL PEAK 6(4P16.3) WILD-TYPE	352	171	54	105	32

Figure S327. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_4p16.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S328. Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 6(4P16.3) MUTATED	84	40	50	15	29
DEL PEAK 6(4P16.3) WILD-TYPE	48	157	127	73	99

Figure S328. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4p16.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S329. Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 6(4P16.3) MUTATED	77	38	25
DEL PEAK 6(4P16.3) WILD-TYPE	72	94	92

Figure S329. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4p16.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S330. Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 6(4P16.3) MUTATED	18	25	54	32	11
DEL PEAK 6(4P16.3) WILD-TYPE	46	81	36	75	20

Figure S330. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4p16.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S331. Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 6(4P16.3) MUTATED	117	20	54	70	53	7	7
DEL PEAK 6(4P16.3) WILD-TYPE	73	123	180	91	191	45	9

Figure S331. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4p16.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S332. Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 6(4P16.3) MUTATED	110	38	37	74	39	30
DEL PEAK 6(4P16.3) WILD-TYPE	68	205	160	106	145	28

Figure S332. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S333. Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 6(4P16.3) MUTATED	50	113	156
DEL PEAK 6(4P16.3) WILD-TYPE	256	309	141

Figure S333. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4p16.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S334. Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 6(4P16.3) MUTATED	23	35	124	84	53
DEL PEAK 6(4P16.3) WILD-TYPE	151	151	281	50	73

Figure S334. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4p16.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S335. Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 6(4P16.3) MUTATED	65	48	111
DEL PEAK 6(4P16.3) WILD-TYPE	184	208	98

Figure S335. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4p16.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S336. Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 6(4P16.3) MUTATED	76	13	62	23	20	30
DEL PEAK 6(4P16.3) WILD-TYPE	51	54	131	112	105	37

Figure S336. Get High-res Image Gene #34: 'del_4p16.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_4q35.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S337. Gene #35: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 7(4Q35.2) MUTATED	7	10	26	52	24	32	10	9
DEL PEAK 7(4Q35.2) WILD-TYPE	14	26	93	44	85	40	10	31

Figure S337. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_4q35.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S338. Gene #35: 'del_4q35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 7(4Q35.2) MUTATED	26	32	52	47	13
DEL PEAK 7(4Q35.2) WILD-TYPE	75	120	62	41	45

Figure S338. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_4q35.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S339. Gene #35: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 7(4Q35.2) MUTATED	50	60	50	167	10
DEL PEAK 7(4Q35.2) WILD-TYPE	349	180	49	97	32

Figure S339. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_4q35.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S340. Gene #35: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 7(4Q35.2) MUTATED	85	37	43	20	37
DEL PEAK 7(4Q35.2) WILD-TYPE	47	160	134	68	91

Figure S340. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_4q35.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S341. Gene #35: 'del_4q35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 7(4Q35.2) MUTATED	79	35	26
DEL PEAK 7(4Q35.2) WILD-TYPE	70	97	91

Figure S341. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_4q35.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S342. Gene #35: 'del_4q35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 7(4Q35.2) MUTATED	15	25	52	37	11
DEL PEAK 7(4Q35.2) WILD-TYPE	49	81	38	70	20

Figure S342. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_4q35.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S343. Gene #35: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 7(4Q35.2) MUTATED	119	20	60	68	53	7	8
DEL PEAK 7(4Q35.2) WILD-TYPE	71	123	174	93	191	45	8

Figure S343. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_4q35.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S344. Gene #35: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 7(4Q35.2) MUTATED	113	42	42	81	34	23
DEL PEAK 7(4Q35.2) WILD-TYPE	65	201	155	99	150	35

Figure S344. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S345. Gene #35: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 7(4Q35.2) MUTATED	55	111	158
DEL PEAK 7(4Q35.2) WILD-TYPE	251	311	139

Figure S345. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_4q35.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S346. Gene #35: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 7(4Q35.2) MUTATED	23	36	121	88	56
DEL PEAK 7(4Q35.2) WILD-TYPE	151	150	284	46	70

Figure S346. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_4q35.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S347. Gene #35: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 7(4Q35.2) MUTATED	63	49	113
DEL PEAK 7(4Q35.2) WILD-TYPE	186	207	96

Figure S347. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_4q35.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S348. Gene #35: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 7(4Q35.2) MUTATED	79	14	68	20	19	25
DEL PEAK 7(4Q35.2) WILD-TYPE	48	53	125	115	106	42

Figure S348. Get High-res Image Gene #35: 'del_4q35.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q11.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S349. Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 8(5Q11.2) MUTATED	3	5	19	69	7	26	3	4
DEL PEAK 8(5Q11.2) WILD-TYPE	18	31	100	27	102	46	17	36

Figure S349. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q11.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S350. Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 8(5Q11.2) MUTATED	18	15	38	63	2
DEL PEAK 8(5Q11.2) WILD-TYPE	83	137	76	25	56

Figure S350. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S351. Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 8(5Q11.2) MUTATED	29	38	8	187	10
DEL PEAK 8(5Q11.2) WILD-TYPE	370	202	91	77	32

Figure S351. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q11.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S352. Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 8(5Q11.2) MUTATED	99	16	30	9	32
DEL PEAK 8(5Q11.2) WILD-TYPE	33	181	147	79	96

Figure S352. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q11.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S353. Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 8(5Q11.2) MUTATED	80	12	23
DEL PEAK 8(5Q11.2) WILD-TYPE	69	120	94

Figure S353. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q11.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S354. Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 8(5Q11.2) MUTATED	4	14	64	23	10
DEL PEAK 8(5Q11.2) WILD-TYPE	60	92	26	84	21

Figure S354. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q11.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S355. Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 8(5Q11.2) MUTATED	137	8	18	55	44	4	5
DEL PEAK 8(5Q11.2) WILD-TYPE	53	135	216	106	200	48	11

Figure S355. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S356. Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 8(5Q11.2) MUTATED	134	19	10	54	29	25
DEL PEAK 8(5Q11.2) WILD-TYPE	44	224	187	126	155	33

Figure S356. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S357. Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 8(5Q11.2) MUTATED	23	59	178
DEL PEAK 8(5Q11.2) WILD-TYPE	283	363	119

Figure S357. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S358. Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 8(5Q11.2) MUTATED	7	19	71	105	58
DEL PEAK 8(5Q11.2) WILD-TYPE	167	167	334	29	68

Figure S358. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q11.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S359. Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 8(5Q11.2) MUTATED	37	18	131
DEL PEAK 8(5Q11.2) WILD-TYPE	212	238	78

Figure S359. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S360. Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 8(5Q11.2) MUTATED	93	6	33	21	4	29
DEL PEAK 8(5Q11.2) WILD-TYPE	34	61	160	114	121	38

Figure S360. Get High-res Image Gene #36: 'del_5q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_5q21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S361. Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 9(5Q21.3) MUTATED	2	5	19	71	7	24	5	2
DEL PEAK 9(5Q21.3) WILD-TYPE	19	31	100	25	102	48	15	38

Figure S361. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_5q21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S362. Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 9(5Q21.3) MUTATED	18	13	36	66	2
DEL PEAK 9(5Q21.3) WILD-TYPE	83	139	78	22	56

Figure S362. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_5q21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S363. Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 9(5Q21.3) MUTATED	23	32	7	194	8
DEL PEAK 9(5Q21.3) WILD-TYPE	376	208	92	70	34

Figure S363. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_5q21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S364. Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 9(5Q21.3) MUTATED	106	10	28	6	30
DEL PEAK 9(5Q21.3) WILD-TYPE	26	187	149	82	98

Figure S364. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_5q21.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S365. Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 9(5Q21.3) MUTATED	78	12	23
DEL PEAK 9(5Q21.3) WILD-TYPE	71	120	94

Figure S365. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_5q21.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S366. Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 9(5Q21.3) MUTATED	5	16	62	21	9
DEL PEAK 9(5Q21.3) WILD-TYPE	59	90	28	86	22

Figure S366. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_5q21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S367. Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 9(5Q21.3) MUTATED	144	8	12	50	39	4	6
DEL PEAK 9(5Q21.3) WILD-TYPE	46	135	222	111	205	48	10

Figure S367. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_5q21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S368. Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 9(5Q21.3) MUTATED	139	17	7	49	28	23
DEL PEAK 9(5Q21.3) WILD-TYPE	39	226	190	131	156	35

Figure S368. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S369. Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 9(5Q21.3) MUTATED	18	55	181
DEL PEAK 9(5Q21.3) WILD-TYPE	288	367	116

Figure S369. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_5q21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S370. Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 9(5Q21.3) MUTATED	5	14	68	109	58
DEL PEAK 9(5Q21.3) WILD-TYPE	169	172	337	25	68

Figure S370. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_5q21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S371. Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 9(5Q21.3) MUTATED	28	18	129
DEL PEAK 9(5Q21.3) WILD-TYPE	221	238	80

Figure S371. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_5q21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S372. Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 9(5Q21.3) MUTATED	97	6	28	14	3	27
DEL PEAK 9(5Q21.3) WILD-TYPE	30	61	165	121	122	40

Figure S372. Get High-res Image Gene #37: 'del_5q21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6p25.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S373. Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 10(6P25.3) MUTATED	41	73	19	61	8
DEL PEAK 10(6P25.3) WILD-TYPE	358	167	80	203	34

Figure S373. Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_6p25.3' versus 'MRNASEQ_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.23

Table S374. Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 10(6P25.3) MUTATED	45	15	41	29	64	6	1
DEL PEAK 10(6P25.3) WILD-TYPE	145	128	193	132	180	46	15

Figure S374. Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6p25.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.074

Table S375. Gene #38: 'del_6p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 10(6P25.3) MUTATED	31	5	55	22	16	14
DEL PEAK 10(6P25.3) WILD-TYPE	96	62	138	113	109	53

Figure S375. Get High-res Image Gene #38: 'del_6p25.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q15' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S376. Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 11(6Q15) MUTATED	6	13	63	20	24	29	4	16
DEL PEAK 11(6Q15) WILD-TYPE	15	23	56	76	85	43	16	24

Figure S376. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_6q15' versus 'MRNA_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.069

Table S377. Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 11(6Q15) MUTATED	50	51	42	18	14
DEL PEAK 11(6Q15) WILD-TYPE	51	101	72	70	44

Figure S377. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_6q15' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S378. Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 11(6Q15) MUTATED	85	152	30	51	23
DEL PEAK 11(6Q15) WILD-TYPE	314	88	69	213	19

Figure S378. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q15' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S379. Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 11(6Q15) MUTATED	26	81	73	21	25
DEL PEAK 11(6Q15) WILD-TYPE	106	116	104	67	103

Figure S379. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_6q15' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S380. Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 11(6Q15) MUTATED	31	42	72	56	123	12	4
DEL PEAK 11(6Q15) WILD-TYPE	159	101	162	105	121	40	12

Figure S380. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q15' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S381. Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 11(6Q15) MUTATED	28	79	50	65	98	20
DEL PEAK 11(6Q15) WILD-TYPE	150	164	147	115	86	38

Figure S381. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S382. Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 11(6Q15) MUTATED	47	81	150	21	39
DEL PEAK 11(6Q15) WILD-TYPE	127	105	255	113	87

Figure S382. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_6q15' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S383. Gene #39: 'del_6q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 11(6Q15) MUTATED	21	19	82	56	33	20
DEL PEAK 11(6Q15) WILD-TYPE	106	48	111	79	92	47

Figure S383. Get High-res Image Gene #39: 'del_6q15' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_6q27' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S384. Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 12(6Q27) MUTATED	94	127	28	88	25
DEL PEAK 12(6Q27) WILD-TYPE	305	113	71	176	17

Figure S384. Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #3: 'CN_CNMF'

'del_6q27' versus 'MRNASEQ_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.24

Table S385. Gene #40: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 12(6Q27) MUTATED	66	44	65	59	110	12	4
DEL PEAK 12(6Q27) WILD-TYPE	124	99	169	102	134	40	12

Figure S385. Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_6q27' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.055

Table S386. Gene #40: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 12(6Q27) MUTATED	61	82	46	62	82	27
DEL PEAK 12(6Q27) WILD-TYPE	117	161	151	118	102	31

Figure S386. Get High-res Image Gene #40: 'del_6q27' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S387. Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 13(7P22.3) MUTATED	4	3	24	25	2	12	2	4
DEL PEAK 13(7P22.3) WILD-TYPE	17	33	95	71	107	60	18	36

Figure S387. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_7p22.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S388. Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 13(7P22.3) MUTATED	20	8	22	24	2
DEL PEAK 13(7P22.3) WILD-TYPE	81	144	92	64	56

Figure S388. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7p22.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S389. Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 13(7P22.3) MUTATED	12	51	4	65	2
DEL PEAK 13(7P22.3) WILD-TYPE	387	189	95	199	40

Figure S389. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_7p22.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S390. Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 13(7P22.3) MUTATED	30	12	25	6	5
DEL PEAK 13(7P22.3) WILD-TYPE	102	185	152	82	123

Figure S390. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_7p22.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S391. Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 13(7P22.3) MUTATED	49	6	11	27	37	1	1
DEL PEAK 13(7P22.3) WILD-TYPE	141	137	223	134	207	51	15

Figure S391. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7p22.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S392. Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 13(7P22.3) MUTATED	47	9	12	31	28	5
DEL PEAK 13(7P22.3) WILD-TYPE	131	234	185	149	156	53

Figure S392. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S393. Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 13(7P22.3) MUTATED	8	55	67
DEL PEAK 13(7P22.3) WILD-TYPE	298	367	230

Figure S393. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7p22.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S394. Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 13(7P22.3) MUTATED	3	9	58	38	22
DEL PEAK 13(7P22.3) WILD-TYPE	171	177	347	96	104

Figure S394. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7p22.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S395. Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 13(7P22.3) MUTATED	22	12	43
DEL PEAK 13(7P22.3) WILD-TYPE	227	244	166

Figure S395. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7p22.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S396. Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 13(7P22.3) MUTATED	32	1	24	13	2	5
DEL PEAK 13(7P22.3) WILD-TYPE	95	66	169	122	123	62

Figure S396. Get High-res Image Gene #41: 'del_7p22.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_7q36.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S397. Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 14(7Q36.1) MUTATED	16	17	45	17	7
DEL PEAK 14(7Q36.1) WILD-TYPE	85	135	69	71	51

Figure S397. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_7q36.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S398. Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 14(7Q36.1) MUTATED	37	65	13	74	6
DEL PEAK 14(7Q36.1) WILD-TYPE	362	175	86	190	36

Figure S398. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_7q36.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S399. Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 14(7Q36.1) MUTATED	44	15	31	52	45	4	2
DEL PEAK 14(7Q36.1) WILD-TYPE	146	128	203	109	199	48	14

Figure S399. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_7q36.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S400. Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 14(7Q36.1) MUTATED	38	28	23	48	38	18
DEL PEAK 14(7Q36.1) WILD-TYPE	140	215	174	132	146	40

Figure S400. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S401. Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 14(7Q36.1) MUTATED	25	82	83
DEL PEAK 14(7Q36.1) WILD-TYPE	281	340	214

Figure S401. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_7q36.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S402. Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 14(7Q36.1) MUTATED	11	24	88	29	38
DEL PEAK 14(7Q36.1) WILD-TYPE	163	162	317	105	88

Figure S402. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_7q36.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S403. Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 14(7Q36.1) MUTATED	46	22	60
DEL PEAK 14(7Q36.1) WILD-TYPE	203	234	149

Figure S403. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_7q36.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S404. Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 14(7Q36.1) MUTATED	33	7	43	20	5	20
DEL PEAK 14(7Q36.1) WILD-TYPE	94	60	150	115	120	47

Figure S404. Get High-res Image Gene #42: 'del_7q36.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p23.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S405. Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 15(8P23.2) MUTATED	12	15	78	64	29	47	13	18
DEL PEAK 15(8P23.2) WILD-TYPE	9	21	41	32	80	25	7	22

Figure S405. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S406. Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 15(8P23.2) MUTATED	67	59	78	57	15
DEL PEAK 15(8P23.2) WILD-TYPE	34	93	36	31	43

Figure S406. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S407. Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 15(8P23.2) MUTATED	128	169	26	185	34
DEL PEAK 15(8P23.2) WILD-TYPE	271	71	73	79	8

Figure S407. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S408. Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 15(8P23.2) MUTATED	87	81	102	26	63
DEL PEAK 15(8P23.2) WILD-TYPE	45	116	75	62	65

Figure S408. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_8p23.2' versus 'RPPA_CHIERARCHICAL'

P value = 0.00074 (Fisher's exact test), Q value = 0.13

Table S409. Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 15(8P23.2) MUTATED	22	57	58	66	22
DEL PEAK 15(8P23.2) WILD-TYPE	42	49	32	41	9

Figure S409. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S410. Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 15(8P23.2) MUTATED	119	53	73	109	151	22	12
DEL PEAK 15(8P23.2) WILD-TYPE	71	90	161	52	93	30	4

Figure S410. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S411. Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 15(8P23.2) MUTATED	112	95	51	119	115	47
DEL PEAK 15(8P23.2) WILD-TYPE	66	148	146	61	69	11

Figure S411. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S412. Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 15(8P23.2) MUTATED	116	220	194
DEL PEAK 15(8P23.2) WILD-TYPE	190	202	103

Figure S412. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p23.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S413. Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 15(8P23.2) MUTATED	55	85	215	86	89
DEL PEAK 15(8P23.2) WILD-TYPE	119	101	190	48	37

Figure S413. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p23.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S414. Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 15(8P23.2) MUTATED	123	101	138
DEL PEAK 15(8P23.2) WILD-TYPE	126	155	71

Figure S414. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S415. Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 15(8P23.2) MUTATED	81	21	95	73	42	50
DEL PEAK 15(8P23.2) WILD-TYPE	46	46	98	62	83	17

Figure S415. Get High-res Image Gene #43: 'del_8p23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_8p11.21' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.021

Table S416. Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 16(8P11.21) MUTATED	4	4	23	23	9	27	7	7
DEL PEAK 16(8P11.21) WILD-TYPE	17	32	96	73	100	45	13	33

Figure S416. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_8p11.21' versus 'MRNA_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.052

Table S417. Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 16(8P11.21) MUTATED	21	20	37	21	5
DEL PEAK 16(8P11.21) WILD-TYPE	80	132	77	67	53

Figure S417. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_8p11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S418. Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 16(8P11.21) MUTATED	45	56	13	84	1
DEL PEAK 16(8P11.21) WILD-TYPE	354	184	86	180	41

Figure S418. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #3: 'CN_CNMF'

'del_8p11.21' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.035

Table S419. Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 16(8P11.21) MUTATED	5	21	21	24	16
DEL PEAK 16(8P11.21) WILD-TYPE	59	85	69	83	15

Figure S419. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_8p11.21' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S420. Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 16(8P11.21) MUTATED	38	21	25	65	36	9	5
DEL PEAK 16(8P11.21) WILD-TYPE	152	122	209	96	208	43	11

Figure S420. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_8p11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S421. Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 16(8P11.21) MUTATED	35	30	20	59	30	25
DEL PEAK 16(8P11.21) WILD-TYPE	143	213	177	121	154	33

Figure S421. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0083

Table S422. Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 16(8P11.21) MUTATED	34	86	77
DEL PEAK 16(8P11.21) WILD-TYPE	272	336	220

Figure S422. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_8p11.21' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S423. Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 16(8P11.21) MUTATED	16	20	87	24	50
DEL PEAK 16(8P11.21) WILD-TYPE	158	166	318	110	76

Figure S423. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_8p11.21' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S424. Gene #44: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 16(8P11.21) MUTATED	58	27	56
DEL PEAK 16(8P11.21) WILD-TYPE	191	229	153

Figure S424. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_8p11.21' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S425. Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 16(8P11.21) MUTATED	28	7	52	10	17	27
DEL PEAK 16(8P11.21) WILD-TYPE	99	60	141	125	108	40

Figure S425. Get High-res Image Gene #44: 'del_8p11.21' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p23' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S426. Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 17(9P23) MUTATED	9	15	57	21	22	34	10	5
DEL PEAK 17(9P23) WILD-TYPE	12	21	62	75	87	38	10	35

Figure S426. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p23' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S427. Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 17(9P23) MUTATED	49	36	61	17	10
DEL PEAK 17(9P23) WILD-TYPE	52	116	53	71	48

Figure S427. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S428. Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 17(9P23) MUTATED	43	153	18	97	8
DEL PEAK 17(9P23) WILD-TYPE	356	87	81	167	34

Figure S428. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S429. Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 17(9P23) MUTATED	37	43	90	14	25
DEL PEAK 17(9P23) WILD-TYPE	95	154	87	74	103

Figure S429. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p23' versus 'RPPA_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.14

Table S430. Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 17(9P23) MUTATED	15	31	26	53	15
DEL PEAK 17(9P23) WILD-TYPE	49	75	64	54	16

Figure S430. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9p23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S431. Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 17(9P23) MUTATED	41	26	43	74	118	9	8
DEL PEAK 17(9P23) WILD-TYPE	149	117	191	87	126	43	8

Figure S431. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S432. Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 17(9P23) MUTATED	34	41	29	92	94	29
DEL PEAK 17(9P23) WILD-TYPE	144	202	168	88	90	29

Figure S432. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S433. Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 17(9P23) MUTATED	56	156	100
DEL PEAK 17(9P23) WILD-TYPE	250	266	197

Figure S433. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S434. Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 17(9P23) MUTATED	17	50	161	21	63
DEL PEAK 17(9P23) WILD-TYPE	157	136	244	113	63

Figure S434. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p23' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.025

Table S435. Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 17(9P23) MUTATED	83	50	72
DEL PEAK 17(9P23) WILD-TYPE	166	206	137

Figure S435. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S436. Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 17(9P23) MUTATED	28	8	75	42	14	38
DEL PEAK 17(9P23) WILD-TYPE	99	59	118	93	111	29

Figure S436. Get High-res Image Gene #45: 'del_9p23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9p21.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S437. Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 18(9P21.3) MUTATED	9	12	62	33	24	38	8	6
DEL PEAK 18(9P21.3) WILD-TYPE	12	24	57	63	85	34	12	34

Figure S437. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9p21.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S438. Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 18(9P21.3) MUTATED	53	34	65	28	12
DEL PEAK 18(9P21.3) WILD-TYPE	48	118	49	60	46

Figure S438. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9p21.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S439. Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 18(9P21.3) MUTATED	50	158	20	120	9
DEL PEAK 18(9P21.3) WILD-TYPE	349	82	79	144	33

Figure S439. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_9p21.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S440. Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 18(9P21.3) MUTATED	51	49	86	14	28
DEL PEAK 18(9P21.3) WILD-TYPE	81	148	91	74	100

Figure S440. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S441. Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 18(9P21.3) MUTATED	66	25	47	78	123	9	7
DEL PEAK 18(9P21.3) WILD-TYPE	124	118	187	83	121	43	9

Figure S441. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9p21.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S442. Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 18(9P21.3) MUTATED	60	39	34	94	97	31
DEL PEAK 18(9P21.3) WILD-TYPE	118	204	163	86	87	27

Figure S442. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S443. Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 18(9P21.3) MUTATED	55	169	123
DEL PEAK 18(9P21.3) WILD-TYPE	251	253	174

Figure S443. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9p21.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S444. Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 18(9P21.3) MUTATED	19	52	167	42	67
DEL PEAK 18(9P21.3) WILD-TYPE	155	134	238	92	59

Figure S444. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9p21.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S445. Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 18(9P21.3) MUTATED	87	52	88
DEL PEAK 18(9P21.3) WILD-TYPE	162	204	121

Figure S445. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9p21.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S446. Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 18(9P21.3) MUTATED	44	9	76	47	12	39
DEL PEAK 18(9P21.3) WILD-TYPE	83	58	117	88	113	28

Figure S446. Get High-res Image Gene #46: 'del_9p21.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q21.11' versus 'MRNA_CNMF'

P value = 0.00115 (Fisher's exact test), Q value = 0.19

Table S447. Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 19(9Q21.11) MUTATED	5	6	42	41	24	27	7	5
DEL PEAK 19(9Q21.11) WILD-TYPE	16	30	77	55	85	45	13	35

Figure S447. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q21.11' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S448. Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 19(9Q21.11) MUTATED	37	25	50	35	10
DEL PEAK 19(9Q21.11) WILD-TYPE	64	127	64	53	48

Figure S448. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q21.11' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S449. Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 19(9Q21.11) MUTATED	36	110	21	110	12
DEL PEAK 19(9Q21.11) WILD-TYPE	363	130	78	154	30

Figure S449. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q21.11' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S450. Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 19(9Q21.11) MUTATED	55	40	54	12	26
DEL PEAK 19(9Q21.11) WILD-TYPE	77	157	123	76	102

Figure S450. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q21.11' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S451. Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 19(9Q21.11) MUTATED	69	33	22
DEL PEAK 19(9Q21.11) WILD-TYPE	80	99	95

Figure S451. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q21.11' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S452. Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 19(9Q21.11) MUTATED	74	15	46	50	90	7	7
DEL PEAK 19(9Q21.11) WILD-TYPE	116	128	188	111	154	45	9

Figure S452. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q21.11' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S453. Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 19(9Q21.11) MUTATED	68	31	26	69	73	22
DEL PEAK 19(9Q21.11) WILD-TYPE	110	212	171	111	111	36

Figure S453. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S454. Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 19(9Q21.11) MUTATED	42	117	123
DEL PEAK 19(9Q21.11) WILD-TYPE	264	305	174

Figure S454. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q21.11' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S455. Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 19(9Q21.11) MUTATED	13	36	121	54	58
DEL PEAK 19(9Q21.11) WILD-TYPE	161	150	284	80	68

Figure S455. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q21.11' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S456. Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 19(9Q21.11) MUTATED	59	43	85
DEL PEAK 19(9Q21.11) WILD-TYPE	190	213	124

Figure S456. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q21.11' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S457. Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 19(9Q21.11) MUTATED	50	5	53	36	10	33
DEL PEAK 19(9Q21.11) WILD-TYPE	77	62	140	99	115	34

Figure S457. Get High-res Image Gene #47: 'del_9q21.11' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_9q34.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S458. Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 20(9Q34.2) MUTATED	6	4	40	55	23	18	7	4
DEL PEAK 20(9Q34.2) WILD-TYPE	15	32	79	41	86	54	13	36

Figure S458. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_9q34.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S459. Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 20(9Q34.2) MUTATED	36	23	38	50	10
DEL PEAK 20(9Q34.2) WILD-TYPE	65	129	76	38	48

Figure S459. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_9q34.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S460. Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 20(9Q34.2) MUTATED	25	98	17	141	12
DEL PEAK 20(9Q34.2) WILD-TYPE	374	142	82	123	30

Figure S460. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_9q34.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S461. Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 20(9Q34.2) MUTATED	74	37	47	10	21
DEL PEAK 20(9Q34.2) WILD-TYPE	58	160	130	78	107

Figure S461. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_9q34.2' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S462. Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 20(9Q34.2) MUTATED	68	33	21
DEL PEAK 20(9Q34.2) WILD-TYPE	81	99	96

Figure S462. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_9q34.2' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S463. Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 20(9Q34.2) MUTATED	12	20	50	37	3
DEL PEAK 20(9Q34.2) WILD-TYPE	52	86	40	70	28

Figure S463. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_9q34.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S464. Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 20(9Q34.2) MUTATED	107	10	45	37	82	4	7
DEL PEAK 20(9Q34.2) WILD-TYPE	83	133	189	124	162	48	9

Figure S464. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_9q34.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S465. Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 20(9Q34.2) MUTATED	101	23	27	58	68	15
DEL PEAK 20(9Q34.2) WILD-TYPE	77	220	170	122	116	43

Figure S465. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S466. Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 20(9Q34.2) MUTATED	34	108	142
DEL PEAK 20(9Q34.2) WILD-TYPE	272	314	155

Figure S466. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_9q34.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S467. Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 20(9Q34.2) MUTATED	13	35	106	79	51
DEL PEAK 20(9Q34.2) WILD-TYPE	161	151	299	55	75

Figure S467. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_9q34.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S468. Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 20(9Q34.2) MUTATED	51	36	104
DEL PEAK 20(9Q34.2) WILD-TYPE	198	220	105

Figure S468. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_9q34.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S469. Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 20(9Q34.2) MUTATED	72	5	49	29	10	26
DEL PEAK 20(9Q34.2) WILD-TYPE	55	62	144	106	115	41

Figure S469. Get High-res Image Gene #48: 'del_9q34.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q23.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S470. Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 21(10Q23.31) MUTATED	7	6	36	49	20	21	7	3
DEL PEAK 21(10Q23.31) WILD-TYPE	14	30	83	47	89	51	13	37

Figure S470. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q23.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S471. Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 21(10Q23.31) MUTATED	28	29	39	45	8
DEL PEAK 21(10Q23.31) WILD-TYPE	73	123	75	43	50

Figure S471. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S472. Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 21(10Q23.31) MUTATED	50	82	27	138	16
DEL PEAK 21(10Q23.31) WILD-TYPE	349	158	72	126	26

Figure S472. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q23.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S473. Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 21(10Q23.31) MUTATED	76	40	65	17	26
DEL PEAK 21(10Q23.31) WILD-TYPE	56	157	112	71	102

Figure S473. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q23.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S474. Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 21(10Q23.31) MUTATED	68	30	20
DEL PEAK 21(10Q23.31) WILD-TYPE	81	102	97

Figure S474. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q23.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S475. Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 21(10Q23.31) MUTATED	12	17	45	34	10
DEL PEAK 21(10Q23.31) WILD-TYPE	52	89	45	73	21

Figure S475. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S476. Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 21(10Q23.31) MUTATED	99	23	41	62	80	4	2
DEL PEAK 21(10Q23.31) WILD-TYPE	91	120	193	99	164	48	14

Figure S476. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q23.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S477. Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 21(10Q23.31) MUTATED	94	37	30	71	57	22
DEL PEAK 21(10Q23.31) WILD-TYPE	84	206	167	109	127	36

Figure S477. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S478. Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 21(10Q23.31) MUTATED	64	104	136
DEL PEAK 21(10Q23.31) WILD-TYPE	242	318	161

Figure S478. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q23.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S479. Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 21(10Q23.31) MUTATED	22	40	113	72	57
DEL PEAK 21(10Q23.31) WILD-TYPE	152	146	292	62	69

Figure S479. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q23.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S480. Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 21(10Q23.31) MUTATED	59	53	100
DEL PEAK 21(10Q23.31) WILD-TYPE	190	203	109

Figure S480. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q23.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S481. Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 21(10Q23.31) MUTATED	71	10	49	38	20	24
DEL PEAK 21(10Q23.31) WILD-TYPE	56	57	144	97	105	43

Figure S481. Get High-res Image Gene #49: 'del_10q23.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_10q26.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S482. Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 22(10Q26.3) MUTATED	8	7	38	55	14	22	6	4
DEL PEAK 22(10Q26.3) WILD-TYPE	13	29	81	41	95	50	14	36

Figure S482. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_10q26.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S483. Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 22(10Q26.3) MUTATED	31	23	44	49	7
DEL PEAK 22(10Q26.3) WILD-TYPE	70	129	70	39	51

Figure S483. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S484. Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 22(10Q26.3) MUTATED	47	88	23	142	11
DEL PEAK 22(10Q26.3) WILD-TYPE	352	152	76	122	31

Figure S484. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S485. Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 22(10Q26.3) MUTATED	75	37	68	12	24
DEL PEAK 22(10Q26.3) WILD-TYPE	57	160	109	76	104

Figure S485. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_10q26.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S486. Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 22(10Q26.3) MUTATED	73	28	24
DEL PEAK 22(10Q26.3) WILD-TYPE	76	104	93

Figure S486. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_10q26.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S487. Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 22(10Q26.3) MUTATED	11	16	48	36	14
DEL PEAK 22(10Q26.3) WILD-TYPE	53	90	42	71	17

Figure S487. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S488. Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 22(10Q26.3) MUTATED	105	17	34	66	79	7	2
DEL PEAK 22(10Q26.3) WILD-TYPE	85	126	200	95	165	45	14

Figure S488. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S489. Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 22(10Q26.3) MUTATED	96	33	27	76	53	25
DEL PEAK 22(10Q26.3) WILD-TYPE	82	210	170	104	131	33

Figure S489. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S490. Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 22(10Q26.3) MUTATED	55	105	140
DEL PEAK 22(10Q26.3) WILD-TYPE	251	317	157

Figure S490. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_10q26.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S491. Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 22(10Q26.3) MUTATED	19	35	116	72	58
DEL PEAK 22(10Q26.3) WILD-TYPE	155	151	289	62	68

Figure S491. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_10q26.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S492. Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 22(10Q26.3) MUTATED	66	47	99
DEL PEAK 22(10Q26.3) WILD-TYPE	183	209	110

Figure S492. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_10q26.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S493. Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 22(10Q26.3) MUTATED	68	10	54	34	17	29
DEL PEAK 22(10Q26.3) WILD-TYPE	59	57	139	101	108	38

Figure S493. Get High-res Image Gene #50: 'del_10q26.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11p15.5' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S494. Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 23(11P15.5) MUTATED	3	8	33	48	14	34	7	9
DEL PEAK 23(11P15.5) WILD-TYPE	18	28	86	48	95	38	13	31

Figure S494. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11p15.5' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S495. Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 23(11P15.5) MUTATED	24	32	50	42	8
DEL PEAK 23(11P15.5) WILD-TYPE	77	120	64	46	50

Figure S495. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11p15.5' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S496. Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 23(11P15.5) MUTATED	34	84	19	158	7
DEL PEAK 23(11P15.5) WILD-TYPE	365	156	80	106	35

Figure S496. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #3: 'CN_CNMF'

'del_11p15.5' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S497. Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 23(11P15.5) MUTATED	69	33	57	15	22
DEL PEAK 23(11P15.5) WILD-TYPE	63	164	120	73	106

Figure S497. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11p15.5' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S498. Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 23(11P15.5) MUTATED	77	27	26
DEL PEAK 23(11P15.5) WILD-TYPE	72	105	91

Figure S498. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_11p15.5' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S499. Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 23(11P15.5) MUTATED	11	20	48	36	15
DEL PEAK 23(11P15.5) WILD-TYPE	53	86	42	71	16

Figure S499. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11p15.5' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S500. Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 23(11P15.5) MUTATED	95	21	31	68	73	10	4
DEL PEAK 23(11P15.5) WILD-TYPE	95	122	203	93	171	42	12

Figure S500. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11p15.5' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S501. Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 23(11P15.5) MUTATED	89	41	23	68	53	28
DEL PEAK 23(11P15.5) WILD-TYPE	89	202	174	112	131	30

Figure S501. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S502. Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 23(11P15.5) MUTATED	53	94	147
DEL PEAK 23(11P15.5) WILD-TYPE	253	328	150

Figure S502. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S503. Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 23(11P15.5) MUTATED	18	31	116	69	60
DEL PEAK 23(11P15.5) WILD-TYPE	156	155	289	65	66

Figure S503. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S504. Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 23(11P15.5) MUTATED	53	44	103
DEL PEAK 23(11P15.5) WILD-TYPE	196	212	106

Figure S504. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_11p15.5' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S505. Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 23(11P15.5) MUTATED	64	9	54	31	15	27
DEL PEAK 23(11P15.5) WILD-TYPE	63	58	139	104	110	40

Figure S505. Get High-res Image Gene #51: 'del_11p15.5' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_11q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S506. Gene #52: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 24(11Q13.1) MUTATED	47	89	27	61	9
DEL PEAK 24(11Q13.1) WILD-TYPE	352	151	72	203	33

Figure S506. Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q13.1' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S507. Gene #52: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 24(11Q13.1) MUTATED	31	39	62	11	16
DEL PEAK 24(11Q13.1) WILD-TYPE	101	158	115	77	112

Figure S507. Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S508. Gene #52: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 24(11Q13.1) MUTATED	41	19	33	33	93	10	3
DEL PEAK 24(11Q13.1) WILD-TYPE	149	124	201	128	151	42	13

Figure S508. Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S509. Gene #52: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 24(11Q13.1) MUTATED	38	40	23	45	76	10
DEL PEAK 24(11Q13.1) WILD-TYPE	140	203	174	135	108	48

Figure S509. Get High-res Image Gene #52: 'del_11q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S510. Gene #53: 'del_11q23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 25(11Q23.2) MUTATED	12	21	89	41	36	38	12	22
DEL PEAK 25(11Q23.2) WILD-TYPE	9	15	30	55	73	34	8	18

Figure S510. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_11q23.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S511. Gene #53: 'del_11q23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 25(11Q23.2) MUTATED	77	74	65	38	17
DEL PEAK 25(11Q23.2) WILD-TYPE	24	78	49	50	41

Figure S511. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_11q23.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S512. Gene #53: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 25(11Q23.2) MUTATED	133	198	44	142	17
DEL PEAK 25(11Q23.2) WILD-TYPE	266	42	55	122	25

Figure S512. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_11q23.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S513. Gene #53: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 25(11Q23.2) MUTATED	66	98	124	33	45
DEL PEAK 25(11Q23.2) WILD-TYPE	66	99	53	55	83

Figure S513. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_11q23.2' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S514. Gene #53: 'del_11q23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 25(11Q23.2) MUTATED	20	55	42	75	17
DEL PEAK 25(11Q23.2) WILD-TYPE	44	51	48	32	14

Figure S514. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_11q23.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S515. Gene #53: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 25(11Q23.2) MUTATED	87	60	83	85	184	25	9
DEL PEAK 25(11Q23.2) WILD-TYPE	103	83	151	76	60	27	7

Figure S515. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_11q23.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S516. Gene #53: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 25(11Q23.2) MUTATED	79	114	54	116	146	24
DEL PEAK 25(11Q23.2) WILD-TYPE	99	129	143	64	38	34

Figure S516. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S517. Gene #53: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 25(11Q23.2) MUTATED	66	99	230	61	63
DEL PEAK 25(11Q23.2) WILD-TYPE	108	87	175	73	63

Figure S517. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_11q23.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.2

Table S518. Gene #53: 'del_11q23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 25(11Q23.2) MUTATED	56	23	111	74	49	36
DEL PEAK 25(11Q23.2) WILD-TYPE	71	44	82	61	76	31

Figure S518. Get High-res Image Gene #53: 'del_11q23.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12p13.2' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.085

Table S519. Gene #54: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 26(12P13.2) MUTATED	45	52	14	60	6
DEL PEAK 26(12P13.2) WILD-TYPE	354	188	85	204	36

Figure S519. Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_12p13.2' versus 'MIRSEQ_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.076

Table S520. Gene #54: 'del_12p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 26(12P13.2) MUTATED	37	66	71
DEL PEAK 26(12P13.2) WILD-TYPE	269	356	226

Figure S520. Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12p13.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.077

Table S521. Gene #54: 'del_12p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 26(12P13.2) MUTATED	16	26	68	30	34
DEL PEAK 26(12P13.2) WILD-TYPE	158	160	337	104	92

Figure S521. Get High-res Image Gene #54: 'del_12p13.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S522. Gene #55: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 27(12Q23.1) MUTATED	2	1	14	43	6	23	4	4
DEL PEAK 27(12Q23.1) WILD-TYPE	19	35	105	53	103	49	16	36

Figure S522. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q23.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S523. Gene #55: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 27(12Q23.1) MUTATED	12	10	35	37	3
DEL PEAK 27(12Q23.1) WILD-TYPE	89	142	79	51	55

Figure S523. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q23.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S524. Gene #55: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 27(12Q23.1) MUTATED	29	34	20	112	4
DEL PEAK 27(12Q23.1) WILD-TYPE	370	206	79	152	38

Figure S524. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S525. Gene #55: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 27(12Q23.1) MUTATED	68	15	30	12	14
DEL PEAK 27(12Q23.1) WILD-TYPE	64	182	147	76	114

Figure S525. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q23.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S526. Gene #55: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 27(12Q23.1) MUTATED	50	11	18
DEL PEAK 27(12Q23.1) WILD-TYPE	99	121	99

Figure S526. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q23.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S527. Gene #55: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 27(12Q23.1) MUTATED	5	11	40	16	7
DEL PEAK 27(12Q23.1) WILD-TYPE	59	95	50	91	24

Figure S527. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q23.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S528. Gene #55: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 27(12Q23.1) MUTATED	84	10	22	39	34	6	2
DEL PEAK 27(12Q23.1) WILD-TYPE	106	133	212	122	210	46	14

Figure S528. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S529. Gene #55: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 27(12Q23.1) MUTATED	79	22	11	43	22	20
DEL PEAK 27(12Q23.1) WILD-TYPE	99	221	186	137	162	38

Figure S529. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S530. Gene #55: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 27(12Q23.1) MUTATED	29	54	112
DEL PEAK 27(12Q23.1) WILD-TYPE	277	368	185

Figure S530. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q23.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S531. Gene #55: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 27(12Q23.1) MUTATED	16	11	69	59	40
DEL PEAK 27(12Q23.1) WILD-TYPE	158	175	336	75	86

Figure S531. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q23.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S532. Gene #55: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 27(12Q23.1) MUTATED	32	30	82
DEL PEAK 27(12Q23.1) WILD-TYPE	217	226	127

Figure S532. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q23.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S533. Gene #55: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 27(12Q23.1) MUTATED	57	3	36	14	13	21
DEL PEAK 27(12Q23.1) WILD-TYPE	70	64	157	121	112	46

Figure S533. Get High-res Image Gene #55: 'del_12q23.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_12q24.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S534. Gene #56: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 28(12Q24.31) MUTATED	4	6	12	42	6	20	5	6
DEL PEAK 28(12Q24.31) WILD-TYPE	17	30	107	54	103	52	15	34

Figure S534. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_12q24.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S535. Gene #56: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 28(12Q24.31) MUTATED	10	15	35	37	4
DEL PEAK 28(12Q24.31) WILD-TYPE	91	137	79	51	54

Figure S535. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_12q24.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S536. Gene #56: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 28(12Q24.31) MUTATED	38	31	20	111	5
DEL PEAK 28(12Q24.31) WILD-TYPE	361	209	79	153	37

Figure S536. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_12q24.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S537. Gene #56: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 28(12Q24.31) MUTATED	68	18	26	14	16
DEL PEAK 28(12Q24.31) WILD-TYPE	64	179	151	74	112

Figure S537. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_12q24.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S538. Gene #56: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 28(12Q24.31) MUTATED	49	13	20
DEL PEAK 28(12Q24.31) WILD-TYPE	100	119	97

Figure S538. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_12q24.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S539. Gene #56: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 28(12Q24.31) MUTATED	7	13	36	16	10
DEL PEAK 28(12Q24.31) WILD-TYPE	57	93	54	91	21

Figure S539. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_12q24.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S540. Gene #56: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 28(12Q24.31) MUTATED	82	19	24	42	27	8	2
DEL PEAK 28(12Q24.31) WILD-TYPE	108	124	210	119	217	44	14

Figure S540. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_12q24.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S541. Gene #56: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 28(12Q24.31) MUTATED	77	36	12	40	19	20
DEL PEAK 28(12Q24.31) WILD-TYPE	101	207	185	140	165	38

Figure S541. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S542. Gene #56: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 28(12Q24.31) MUTATED	41	57	104
DEL PEAK 28(12Q24.31) WILD-TYPE	265	365	193

Figure S542. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_12q24.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S543. Gene #56: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 28(12Q24.31) MUTATED	24	12	69	58	39
DEL PEAK 28(12Q24.31) WILD-TYPE	150	174	336	76	87

Figure S543. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_12q24.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S544. Gene #56: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 28(12Q24.31) MUTATED	34	34	76
DEL PEAK 28(12Q24.31) WILD-TYPE	215	222	133

Figure S544. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_12q24.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S545. Gene #56: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 28(12Q24.31) MUTATED	52	3	36	14	19	20
DEL PEAK 28(12Q24.31) WILD-TYPE	75	64	157	121	106	47

Figure S545. Get High-res Image Gene #56: 'del_12q24.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_13q14.2' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S546. Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 29(13Q14.2) MUTATED	8	12	70	60	34	41	9	13
DEL PEAK 29(13Q14.2) WILD-TYPE	13	24	49	36	75	31	11	27

Figure S546. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_13q14.2' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S547. Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 29(13Q14.2) MUTATED	64	47	67	56	13
DEL PEAK 29(13Q14.2) WILD-TYPE	37	105	47	32	45

Figure S547. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_13q14.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S548. Gene #57: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 29(13Q14.2) MUTATED	88	153	62	158	24
DEL PEAK 29(13Q14.2) WILD-TYPE	311	87	37	106	18

Figure S548. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_13q14.2' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S549. Gene #57: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 29(13Q14.2) MUTATED	84	81	97	24	44
DEL PEAK 29(13Q14.2) WILD-TYPE	48	116	80	64	84

Figure S549. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_13q14.2' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S550. Gene #57: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 29(13Q14.2) MUTATED	19	44	58	61	10
DEL PEAK 29(13Q14.2) WILD-TYPE	45	62	32	46	21

Figure S550. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_13q14.2' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S551. Gene #57: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 29(13Q14.2) MUTATED	120	41	86	81	130	16	9
DEL PEAK 29(13Q14.2) WILD-TYPE	70	102	148	80	114	36	7

Figure S551. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_13q14.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S552. Gene #57: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 29(13Q14.2) MUTATED	112	77	60	104	104	26
DEL PEAK 29(13Q14.2) WILD-TYPE	66	166	137	76	80	32

Figure S552. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S553. Gene #57: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 29(13Q14.2) MUTATED	97	206	171
DEL PEAK 29(13Q14.2) WILD-TYPE	209	216	126

Figure S553. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_13q14.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S554. Gene #57: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 29(13Q14.2) MUTATED	45	82	199	89	59
DEL PEAK 29(13Q14.2) WILD-TYPE	129	104	206	45	67

Figure S554. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_13q14.2' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S555. Gene #57: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 29(13Q14.2) MUTATED	111	83	122
DEL PEAK 29(13Q14.2) WILD-TYPE	138	173	87

Figure S555. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_13q14.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S556. Gene #57: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 29(13Q14.2) MUTATED	78	17	98	59	31	33
DEL PEAK 29(13Q14.2) WILD-TYPE	49	50	95	76	94	34

Figure S556. Get High-res Image Gene #57: 'del_13q14.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_14q24.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S557. Gene #58: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 30(14Q24.1) MUTATED	4	7	47	63	10	22	10	8
DEL PEAK 30(14Q24.1) WILD-TYPE	17	29	72	33	99	50	10	32

Figure S557. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_14q24.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S558. Gene #58: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 30(14Q24.1) MUTATED	37	30	41	59	4
DEL PEAK 30(14Q24.1) WILD-TYPE	64	122	73	29	54

Figure S558. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_14q24.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S559. Gene #58: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 30(14Q24.1) MUTATED	48	88	22	169	14
DEL PEAK 30(14Q24.1) WILD-TYPE	351	152	77	95	28

Figure S559. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_14q24.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S560. Gene #58: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 30(14Q24.1) MUTATED	88	38	58	17	31
DEL PEAK 30(14Q24.1) WILD-TYPE	44	159	119	71	97

Figure S560. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_14q24.1' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S561. Gene #58: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 30(14Q24.1) MUTATED	77	27	33
DEL PEAK 30(14Q24.1) WILD-TYPE	72	105	84

Figure S561. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_14q24.1' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S562. Gene #58: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 30(14Q24.1) MUTATED	6	27	58	38	8
DEL PEAK 30(14Q24.1) WILD-TYPE	58	79	32	69	23

Figure S562. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_14q24.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S563. Gene #58: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 30(14Q24.1) MUTATED	126	23	28	52	97	8	6
DEL PEAK 30(14Q24.1) WILD-TYPE	64	120	206	109	147	44	10

Figure S563. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_14q24.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S564. Gene #58: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 30(14Q24.1) MUTATED	121	44	22	75	63	15
DEL PEAK 30(14Q24.1) WILD-TYPE	57	199	175	105	121	43

Figure S564. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S565. Gene #58: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 30(14Q24.1) MUTATED	60	105	166
DEL PEAK 30(14Q24.1) WILD-TYPE	246	317	131

Figure S565. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_14q24.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S566. Gene #58: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 30(14Q24.1) MUTATED	20	41	120	96	54
DEL PEAK 30(14Q24.1) WILD-TYPE	154	145	285	38	72

Figure S566. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_14q24.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S567. Gene #58: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 30(14Q24.1) MUTATED	69	47	122
DEL PEAK 30(14Q24.1) WILD-TYPE	180	209	87

Figure S567. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_14q24.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S568. Gene #58: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 30(14Q24.1) MUTATED	85	12	64	38	14	25
DEL PEAK 30(14Q24.1) WILD-TYPE	42	55	129	97	111	42

Figure S568. Get High-res Image Gene #58: 'del_14q24.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_15q13.1' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S569. Gene #59: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 31(15Q13.1) MUTATED	5	11	41	58	24	34	10	8
DEL PEAK 31(15Q13.1) WILD-TYPE	16	25	78	38	85	38	10	32

Figure S569. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_15q13.1' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S570. Gene #59: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 31(15Q13.1) MUTATED	36	35	54	54	12
DEL PEAK 31(15Q13.1) WILD-TYPE	65	117	60	34	46

Figure S570. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_15q13.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S571. Gene #59: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 31(15Q13.1) MUTATED	44	85	47	175	13
DEL PEAK 31(15Q13.1) WILD-TYPE	355	155	52	89	29

Figure S571. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_15q13.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S572. Gene #59: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 31(15Q13.1) MUTATED	86	45	65	20	29
DEL PEAK 31(15Q13.1) WILD-TYPE	46	152	112	68	99

Figure S572. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_15q13.1' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.016

Table S573. Gene #59: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 31(15Q13.1) MUTATED	80	39	38
DEL PEAK 31(15Q13.1) WILD-TYPE	69	93	79

Figure S573. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_15q13.1' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S574. Gene #59: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 31(15Q13.1) MUTATED	18	29	54	43	13
DEL PEAK 31(15Q13.1) WILD-TYPE	46	77	36	64	18

Figure S574. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_15q13.1' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S575. Gene #59: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 31(15Q13.1) MUTATED	122	24	53	69	80	7	7
DEL PEAK 31(15Q13.1) WILD-TYPE	68	119	181	92	164	45	9

Figure S575. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_15q13.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S576. Gene #59: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 31(15Q13.1) MUTATED	118	47	32	83	62	20
DEL PEAK 31(15Q13.1) WILD-TYPE	60	196	165	97	122	38

Figure S576. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S577. Gene #59: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 31(15Q13.1) MUTATED	53	132	170
DEL PEAK 31(15Q13.1) WILD-TYPE	253	290	127

Figure S577. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_15q13.1' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S578. Gene #59: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 31(15Q13.1) MUTATED	24	35	145	97	54
DEL PEAK 31(15Q13.1) WILD-TYPE	150	151	260	37	72

Figure S578. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_15q13.1' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S579. Gene #59: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 31(15Q13.1) MUTATED	82	46	117
DEL PEAK 31(15Q13.1) WILD-TYPE	167	210	92

Figure S579. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_15q13.1' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S580. Gene #59: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 31(15Q13.1) MUTATED	85	12	78	23	19	28
DEL PEAK 31(15Q13.1) WILD-TYPE	42	55	115	112	106	39

Figure S580. Get High-res Image Gene #59: 'del_15q13.1' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_16q24.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S581. Gene #60: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 32(16Q24.3) MUTATED	16	25	81	27	94	45	13	35
DEL PEAK 32(16Q24.3) WILD-TYPE	5	11	38	69	15	27	7	5

Figure S581. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_16q24.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S582. Gene #60: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 32(16Q24.3) MUTATED	74	124	71	22	45
DEL PEAK 32(16Q24.3) WILD-TYPE	27	28	43	66	13

Figure S582. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_16q24.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S583. Gene #60: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 32(16Q24.3) MUTATED	285	154	81	119	33
DEL PEAK 32(16Q24.3) WILD-TYPE	114	86	18	145	9

Figure S583. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_16q24.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S584. Gene #60: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 32(16Q24.3) MUTATED	53	152	118	61	72
DEL PEAK 32(16Q24.3) WILD-TYPE	79	45	59	27	56

Figure S584. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_16q24.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S585. Gene #60: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 32(16Q24.3) MUTATED	64	103	84
DEL PEAK 32(16Q24.3) WILD-TYPE	85	29	33

Figure S585. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_16q24.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S586. Gene #60: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 32(16Q24.3) MUTATED	54	80	28	74	15
DEL PEAK 32(16Q24.3) WILD-TYPE	10	26	62	33	16

Figure S586. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_16q24.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S587. Gene #60: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 32(16Q24.3) MUTATED	62	111	198	91	153	42	12
DEL PEAK 32(16Q24.3) WILD-TYPE	128	32	36	70	91	10	4

Figure S587. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_16q24.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S588. Gene #60: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 32(16Q24.3) MUTATED	56	191	154	115	126	27
DEL PEAK 32(16Q24.3) WILD-TYPE	122	52	43	65	58	31

Figure S588. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S589. Gene #60: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 32(16Q24.3) MUTATED	229	306	125
DEL PEAK 32(16Q24.3) WILD-TYPE	77	116	172

Figure S589. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_16q24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S590. Gene #60: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 32(16Q24.3) MUTATED	136	136	281	47	60
DEL PEAK 32(16Q24.3) WILD-TYPE	38	50	124	87	66

Figure S590. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_16q24.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S591. Gene #60: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 32(16Q24.3) MUTATED	171	190	92
DEL PEAK 32(16Q24.3) WILD-TYPE	78	66	117

Figure S591. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_16q24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S592. Gene #60: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 32(16Q24.3) MUTATED	45	49	138	79	108	34
DEL PEAK 32(16Q24.3) WILD-TYPE	82	18	55	56	17	33

Figure S592. Get High-res Image Gene #60: 'del_16q24.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17p12' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S593. Gene #61: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 33(17P12) MUTATED	14	27	78	65	33	62	15	24
DEL PEAK 33(17P12) WILD-TYPE	7	9	41	31	76	10	5	16

Figure S593. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17p12' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S594. Gene #61: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 33(17P12) MUTATED	69	86	93	58	12
DEL PEAK 33(17P12) WILD-TYPE	32	66	21	30	46

Figure S594. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17p12' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S595. Gene #61: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 33(17P12) MUTATED	160	189	50	206	24
DEL PEAK 33(17P12) WILD-TYPE	239	51	49	58	18

Figure S595. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #3: 'CN_CNMF'

'del_17p12' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S596. Gene #61: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 33(17P12) MUTATED	87	98	133	43	65
DEL PEAK 33(17P12) WILD-TYPE	45	99	44	45	63

Figure S596. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17p12' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S597. Gene #61: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 33(17P12) MUTATED	116	66	66
DEL PEAK 33(17P12) WILD-TYPE	33	66	51

Figure S597. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17p12' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S598. Gene #61: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 33(17P12) MUTATED	23	57	65	77	26
DEL PEAK 33(17P12) WILD-TYPE	41	49	25	30	5

Figure S598. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17p12' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S599. Gene #61: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 33(17P12) MUTATED	120	77	83	134	173	27	12
DEL PEAK 33(17P12) WILD-TYPE	70	66	151	27	71	25	4

Figure S599. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17p12' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S600. Gene #61: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 33(17P12) MUTATED	113	132	56	148	131	46
DEL PEAK 33(17P12) WILD-TYPE	65	111	141	32	53	12

Figure S600. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S601. Gene #61: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 33(17P12) MUTATED	154	252	212
DEL PEAK 33(17P12) WILD-TYPE	152	170	85

Figure S601. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17p12' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S602. Gene #61: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 33(17P12) MUTATED	72	98	269	91	88
DEL PEAK 33(17P12) WILD-TYPE	102	88	136	43	38

Figure S602. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17p12' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.13

Table S603. Gene #61: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 33(17P12) MUTATED	146	133	145
DEL PEAK 33(17P12) WILD-TYPE	103	123	64

Figure S603. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17p12' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S604. Gene #61: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 33(17P12) MUTATED	78	32	133	74	54	53
DEL PEAK 33(17P12) WILD-TYPE	49	35	60	61	71	14

Figure S604. Get High-res Image Gene #61: 'del_17p12' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_17q21.31' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S605. Gene #62: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 34(17Q21.31) MUTATED	7	17	28	53	13	50	9	15
DEL PEAK 34(17Q21.31) WILD-TYPE	14	19	91	43	96	22	11	25

Figure S605. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_17q21.31' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S606. Gene #62: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 34(17Q21.31) MUTATED	24	49	70	46	3
DEL PEAK 34(17Q21.31) WILD-TYPE	77	103	44	42	55

Figure S606. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_17q21.31' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S607. Gene #62: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 34(17Q21.31) MUTATED	81	79	24	170	8
DEL PEAK 34(17Q21.31) WILD-TYPE	318	161	75	94	34

Figure S607. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #3: 'CN_CNMF'

'del_17q21.31' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S608. Gene #62: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 34(17Q21.31) MUTATED	81	30	63	18	40
DEL PEAK 34(17Q21.31) WILD-TYPE	51	167	114	70	88

Figure S608. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_17q21.31' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S609. Gene #62: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 34(17Q21.31) MUTATED	90	24	44
DEL PEAK 34(17Q21.31) WILD-TYPE	59	108	73

Figure S609. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_17q21.31' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S610. Gene #62: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 34(17Q21.31) MUTATED	10	34	52	36	26
DEL PEAK 34(17Q21.31) WILD-TYPE	54	72	38	71	5

Figure S610. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_17q21.31' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S611. Gene #62: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 34(17Q21.31) MUTATED	101	33	34	114	59	14	6
DEL PEAK 34(17Q21.31) WILD-TYPE	89	110	200	47	185	38	10

Figure S611. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_17q21.31' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S612. Gene #62: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 34(17Q21.31) MUTATED	96	71	16	98	40	40
DEL PEAK 34(17Q21.31) WILD-TYPE	82	172	181	82	144	18

Figure S612. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S613. Gene #62: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 34(17Q21.31) MUTATED	69	124	161
DEL PEAK 34(17Q21.31) WILD-TYPE	237	298	136

Figure S613. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_17q21.31' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S614. Gene #62: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 34(17Q21.31) MUTATED	34	31	154	80	55
DEL PEAK 34(17Q21.31) WILD-TYPE	140	155	251	54	71

Figure S614. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_17q21.31' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S615. Gene #62: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 34(17Q21.31) MUTATED	77	58	115
DEL PEAK 34(17Q21.31) WILD-TYPE	172	198	94

Figure S615. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_17q21.31' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S616. Gene #62: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 34(17Q21.31) MUTATED	68	13	80	31	21	37
DEL PEAK 34(17Q21.31) WILD-TYPE	59	54	113	104	104	30

Figure S616. Get High-res Image Gene #62: 'del_17q21.31' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_18q23' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.02

Table S617. Gene #63: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 35(18Q23) MUTATED	6	13	38	38	18	37	6	9
DEL PEAK 35(18Q23) WILD-TYPE	15	23	81	58	91	35	14	31

Figure S617. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_18q23' versus 'MRNA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.012

Table S618. Gene #63: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 35(18Q23) MUTATED	31	35	54	35	10
DEL PEAK 35(18Q23) WILD-TYPE	70	117	60	53	48

Figure S618. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_18q23' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S619. Gene #63: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 35(18Q23) MUTATED	66	103	36	127	11
DEL PEAK 35(18Q23) WILD-TYPE	333	137	63	137	31

Figure S619. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #3: 'CN_CNMF'

'del_18q23' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S620. Gene #63: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 35(18Q23) MUTATED	59	47	88	17	30
DEL PEAK 35(18Q23) WILD-TYPE	73	150	89	71	98

Figure S620. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_18q23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S621. Gene #63: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 35(18Q23) MUTATED	79	28	45	81	87	16	5
DEL PEAK 35(18Q23) WILD-TYPE	111	115	189	80	157	36	11

Figure S621. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_18q23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S622. Gene #63: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 35(18Q23) MUTATED	75	63	28	100	49	26
DEL PEAK 35(18Q23) WILD-TYPE	103	180	169	80	135	32

Figure S622. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S623. Gene #63: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 35(18Q23) MUTATED	74	137	128
DEL PEAK 35(18Q23) WILD-TYPE	232	285	169

Figure S623. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_18q23' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S624. Gene #63: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 35(18Q23) MUTATED	33	48	141	55	62
DEL PEAK 35(18Q23) WILD-TYPE	141	138	264	79	64

Figure S624. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_18q23' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S625. Gene #63: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 35(18Q23) MUTATED	76	60	93
DEL PEAK 35(18Q23) WILD-TYPE	173	196	116

Figure S625. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_18q23' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S626. Gene #63: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 35(18Q23) MUTATED	56	14	72	27	28	32
DEL PEAK 35(18Q23) WILD-TYPE	71	53	121	108	97	35

Figure S626. Get High-res Image Gene #63: 'del_18q23' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19p13.3' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S627. Gene #64: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 36(19P13.3) MUTATED	7	10	49	56	13	34	6	6
DEL PEAK 36(19P13.3) WILD-TYPE	14	26	70	40	96	38	14	34

Figure S627. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19p13.3' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S628. Gene #64: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 36(19P13.3) MUTATED	45	28	53	52	3
DEL PEAK 36(19P13.3) WILD-TYPE	56	124	61	36	55

Figure S628. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19p13.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S629. Gene #64: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 36(19P13.3) MUTATED	36	124	13	162	15
DEL PEAK 36(19P13.3) WILD-TYPE	363	116	86	102	27

Figure S629. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #3: 'CN_CNMF'

'del_19p13.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S630. Gene #64: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 36(19P13.3) MUTATED	73	35	67	12	34
DEL PEAK 36(19P13.3) WILD-TYPE	59	162	110	76	94

Figure S630. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19p13.3' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S631. Gene #64: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 36(19P13.3) MUTATED	79	37	32
DEL PEAK 36(19P13.3) WILD-TYPE	70	95	85

Figure S631. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19p13.3' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S632. Gene #64: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 36(19P13.3) MUTATED	6	31	49	45	17
DEL PEAK 36(19P13.3) WILD-TYPE	58	75	41	62	14

Figure S632. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19p13.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S633. Gene #64: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 36(19P13.3) MUTATED	109	21	26	70	104	10	9
DEL PEAK 36(19P13.3) WILD-TYPE	81	122	208	91	140	42	7

Figure S633. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19p13.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S634. Gene #64: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 36(19P13.3) MUTATED	105	39	18	98	69	20
DEL PEAK 36(19P13.3) WILD-TYPE	73	204	179	82	115	38

Figure S634. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S635. Gene #64: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 36(19P13.3) MUTATED	47	130	163
DEL PEAK 36(19P13.3) WILD-TYPE	259	292	134

Figure S635. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19p13.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S636. Gene #64: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 36(19P13.3) MUTATED	13	43	139	83	62
DEL PEAK 36(19P13.3) WILD-TYPE	161	143	266	51	64

Figure S636. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19p13.3' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S637. Gene #64: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 36(19P13.3) MUTATED	71	49	117
DEL PEAK 36(19P13.3) WILD-TYPE	178	207	92

Figure S637. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19p13.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S638. Gene #64: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 36(19P13.3) MUTATED	74	8	67	44	12	32
DEL PEAK 36(19P13.3) WILD-TYPE	53	59	126	91	113	35

Figure S638. Get High-res Image Gene #64: 'del_19p13.3' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_19q13.32' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S639. Gene #65: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 37(19Q13.32) MUTATED	4	7	23	26	7	28	1	3
DEL PEAK 37(19Q13.32) WILD-TYPE	17	29	96	70	102	44	19	37

Figure S639. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_19q13.32' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S640. Gene #65: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 37(19Q13.32) MUTATED	26	11	36	24	2
DEL PEAK 37(19Q13.32) WILD-TYPE	75	141	78	64	56

Figure S640. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_19q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S641. Gene #65: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 37(19Q13.32) MUTATED	21	83	7	89	6
DEL PEAK 37(19Q13.32) WILD-TYPE	378	157	92	175	36

Figure S641. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #3: 'CN_CNMF'

'del_19q13.32' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S642. Gene #65: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 37(19Q13.32) MUTATED	47	19	47	8	18
DEL PEAK 37(19Q13.32) WILD-TYPE	85	178	130	80	110

Figure S642. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_19q13.32' versus 'RPPA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.099

Table S643. Gene #65: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 37(19Q13.32) MUTATED	45	20	15
DEL PEAK 37(19Q13.32) WILD-TYPE	104	112	102

Figure S643. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_19q13.32' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0083

Table S644. Gene #65: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 37(19Q13.32) MUTATED	4	12	30	23	11
DEL PEAK 37(19Q13.32) WILD-TYPE	60	94	60	84	20

Figure S644. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_19q13.32' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S645. Gene #65: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 37(19Q13.32) MUTATED	57	8	17	58	61	4	1
DEL PEAK 37(19Q13.32) WILD-TYPE	133	135	217	103	183	48	15

Figure S645. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_19q13.32' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S646. Gene #65: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 37(19Q13.32) MUTATED	57	17	9	56	48	19
DEL PEAK 37(19Q13.32) WILD-TYPE	121	226	188	124	136	39

Figure S646. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S647. Gene #65: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 37(19Q13.32) MUTATED	20	82	97
DEL PEAK 37(19Q13.32) WILD-TYPE	286	340	200

Figure S647. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_19q13.32' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S648. Gene #65: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 37(19Q13.32) MUTATED	7	25	89	46	32
DEL PEAK 37(19Q13.32) WILD-TYPE	167	161	316	88	94

Figure S648. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.32' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S649. Gene #65: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 37(19Q13.32) MUTATED	49	20	73
DEL PEAK 37(19Q13.32) WILD-TYPE	200	236	136

Figure S649. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_19q13.32' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S650. Gene #65: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 37(19Q13.32) MUTATED	43	4	45	22	5	23
DEL PEAK 37(19Q13.32) WILD-TYPE	84	63	148	113	120	44

Figure S650. Get High-res Image Gene #65: 'del_19q13.32' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_20p13' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S651. Gene #66: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 38(20P13) MUTATED	1	3	28	25	3	16	3	1
DEL PEAK 38(20P13) WILD-TYPE	20	33	91	71	106	56	17	39

Figure S651. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_20p13' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S652. Gene #66: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
DEL PEAK 38(20P13) MUTATED	23	9	25	23	0
DEL PEAK 38(20P13) WILD-TYPE	78	143	89	65	58

Figure S652. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'del_20p13' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S653. Gene #66: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 38(20P13) MUTATED	18	44	6	80	8
DEL PEAK 38(20P13) WILD-TYPE	381	196	93	184	34

Figure S653. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #3: 'CN_CNMF'

'del_20p13' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S654. Gene #66: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 38(20P13) MUTATED	44	11	29	8	10
DEL PEAK 38(20P13) WILD-TYPE	88	186	148	80	118

Figure S654. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_20p13' versus 'RPPA_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.049

Table S655. Gene #66: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
DEL PEAK 38(20P13) MUTATED	37	10	17
DEL PEAK 38(20P13) WILD-TYPE	112	122	100

Figure S655. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #5: 'RPPA_CNMF'

'del_20p13' versus 'RPPA_CHIERARCHICAL'

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

Table S656. Gene #66: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
DEL PEAK 38(20P13) MUTATED	5	8	24	20	7
DEL PEAK 38(20P13) WILD-TYPE	59	98	66	87	24

Figure S656. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'del_20p13' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S657. Gene #66: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 38(20P13) MUTATED	56	7	9	27	53	2	1
DEL PEAK 38(20P13) WILD-TYPE	134	136	225	134	191	50	15

Figure S657. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_20p13' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S658. Gene #66: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 38(20P13) MUTATED	55	13	6	35	34	12
DEL PEAK 38(20P13) WILD-TYPE	123	230	191	145	150	46

Figure S658. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S659. Gene #66: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
DEL PEAK 38(20P13) MUTATED	16	48	83
DEL PEAK 38(20P13) WILD-TYPE	290	374	214

Figure S659. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'del_20p13' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S660. Gene #66: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 38(20P13) MUTATED	8	17	48	43	31
DEL PEAK 38(20P13) WILD-TYPE	166	169	357	91	95

Figure S660. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_20p13' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S661. Gene #66: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
DEL PEAK 38(20P13) MUTATED	28	16	60
DEL PEAK 38(20P13) WILD-TYPE	221	240	149

Figure S661. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'del_20p13' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S662. Gene #66: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 38(20P13) MUTATED	41	2	23	18	4	16
DEL PEAK 38(20P13) WILD-TYPE	86	65	170	117	121	51

Figure S662. Get High-res Image Gene #66: 'del_20p13' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_21q11.2' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.039

Table S663. Gene #67: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8
ALL	21	36	119	96	109	72	20	40
DEL PEAK 39(21Q11.2) MUTATED	3	11	37	16	11	23	3	4
DEL PEAK 39(21Q11.2) WILD-TYPE	18	25	82	80	98	49	17	36

Figure S663. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #1: 'MRNA_CNMF'

'del_21q11.2' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S664. Gene #67: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 39(21Q11.2) MUTATED	31	85	17	66	10
DEL PEAK 39(21Q11.2) WILD-TYPE	368	155	82	198	32

Figure S664. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #3: 'CN_CNMF'

'del_21q11.2' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.053

Table S665. Gene #67: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
DEL PEAK 39(21Q11.2) MUTATED	22	38	53	8	18
DEL PEAK 39(21Q11.2) WILD-TYPE	110	159	124	80	110

Figure S665. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'del_21q11.2' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.023

Table S666. Gene #67: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	190	143	234	161	244	52	16
DEL PEAK 39(21Q11.2) MUTATED	31	21	33	44	70	6	3
DEL PEAK 39(21Q11.2) WILD-TYPE	159	122	201	117	174	46	13

Figure S666. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'del_21q11.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S667. Gene #67: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	178	243	197	180	184	58
DEL PEAK 39(21Q11.2) MUTATED	29	35	22	62	45	15
DEL PEAK 39(21Q11.2) WILD-TYPE	149	208	175	118	139	43

Figure S667. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.0097

Table S668. Gene #67: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
DEL PEAK 39(21Q11.2) MUTATED	20	26	105	20	33
DEL PEAK 39(21Q11.2) WILD-TYPE	154	160	300	114	93

Figure S668. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'del_21q11.2' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.12

Table S669. Gene #67: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	127	67	193	135	125	67
DEL PEAK 39(21Q11.2) MUTATED	18	6	52	24	14	17
DEL PEAK 39(21Q11.2) WILD-TYPE	109	61	141	111	111	50

Figure S669. Get High-res Image Gene #67: 'del_21q11.2' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_22q11.1' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S670. Gene #68: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 40(22Q11.1) MUTATED	126	123	64	125	15
DEL PEAK 40(22Q11.1) WILD-TYPE	273	117	35	139	27

Figure S670. Get High-res Image Gene #68: 'del_22q11.1' versus Molecular Subtype #3: 'CN_CNMF'

'del_22q13.32' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0083

Table S671. Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
DEL PEAK 41(22Q13.32) MUTATED	132	134	68	127	20
DEL PEAK 41(22Q13.32) WILD-TYPE	267	106	31	137	22

Figure S671. Get High-res Image Gene #69: 'del_22q13.32' versus Molecular Subtype #3: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 1044
Number of significantly focal cnvs = 69
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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