Correlation between copy number variations of arm-level result 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 variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C128069Z

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.

Summary

Testing the association between copy number variation 80 arm-level events and 12 molecular subtypes across 1044 patients, 601 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain 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'.
1q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
2p gain 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'.
2q gain 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'.
3p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q gain 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'.
4p gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
4q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
5p gain cnv correlated to 'CN_CNMF'.
5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p gain 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'.
6q gain 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'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
8p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
8q gain 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'.
9p gain 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'.
9q gain cnv correlated to 'CN_CNMF'.
10p gain 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'.
10q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12p gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
13q gain cnv correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
14q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
15q gain cnv correlated to 'MIRSEQ_CHIERARCHICAL'.
16p gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
16q gain cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17p gain cnv correlated to 'CN_CNMF'.
17q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p gain 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'.
18q gain 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'.
19p gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
19q gain cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q gain 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'.
21q gain 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'.
22q gain 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'.
xq gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
1p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
1q loss cnv correlated to 'CN_CNMF'.
2p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q loss cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
3p loss 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'.
3q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
4p loss 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'.
4q loss 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'.
5p loss 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'.
5q loss 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'.
6p loss cnv correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
7p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7q loss cnv correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
8p loss 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'.
9p loss 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'.
9q loss 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'.
10p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
12p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
12q loss 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'.
13q loss 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'.
14q loss 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'.
15q loss 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'.
16p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
16q loss 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'.
17p loss 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'.
17q loss 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'.
18p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
18q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p loss 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'.
19q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
22q loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
xq loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level 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, 601 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
1p gain	200 (19%)	844	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0152)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
2p gain	119 (11%)	925	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
2q gain	73 (7%)	971	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
10p gain	205 (20%)	839	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
4p loss	340 (33%)	704	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
5p loss	135 (13%)	909	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
5q loss	222 (21%)	822	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
12q loss	125 (12%)	919	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00018 (0.076)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
14q loss	255 (24%)	789	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
16q loss	580 (56%)	464	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	3e-05 (0.0152)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
17p loss	558 (53%)	486	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0152)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	7e-05 (0.0326)	1e-05 (0.0096)
17q loss	263 (25%)	781	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
6p gain	201 (19%)	843	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	6e-05 (0.0282)	0.00148 (0.466)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
6q gain	146 (14%)	898	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00492 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
18p gain	172 (16%)	872	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	0.00082 (0.284)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
21q gain	190 (18%)	854	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0004 (0.154)	0.0007 (0.251)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
22q gain	95 (9%)	949	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00049 (0.185)	1e-05 (0.0096)	0.00076 (0.268)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
3p loss	181 (17%)	863	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00081 (0.281)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
4q loss	302 (29%)	742	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	9e-05 (0.0409)	0.00146 (0.463)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
8p loss	382 (37%)	662	2e-05 (0.0107)	6e-05 (0.0282)	1e-05 (0.0096)	2e-05 (0.0107)	0.0921 (1.00)	5e-05 (0.0238)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	0.00014 (0.0605)	0.00025 (0.101)
9q loss	278 (27%)	766	0.00018 (0.076)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	0.00109 (0.365)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
19p loss	187 (18%)	857	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0279 (1.00)	0.00011 (0.0484)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
3q gain	208 (20%)	836	0.00026 (0.104)	0.0001 (0.0447)	1e-05 (0.0096)	1e-05 (0.0096)	0.0225 (1.00)	0.038 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
8q gain	516 (49%)	528	4e-05 (0.0196)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.108 (1.00)	0.224 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
9p gain	134 (13%)	910	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0108 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00127 (0.413)	0.00016 (0.0683)
16p gain	458 (44%)	586	0.00019 (0.0788)	0.00192 (0.572)	1e-05 (0.0096)	1e-05 (0.0096)	0.0151 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	4e-05 (0.0196)	1e-05 (0.0096)	8e-05 (0.0367)	7e-05 (0.0326)
18q gain	147 (14%)	897	0.0001 (0.0447)	0.00016 (0.0683)	1e-05 (0.0096)	9e-05 (0.0409)	0.0787 (1.00)	0.00165 (0.503)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	5e-05 (0.0238)	2e-05 (0.0107)
20q gain	438 (42%)	606	0.00021 (0.0865)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0932 (1.00)	0.152 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
9p loss	310 (30%)	734	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00166 (0.503)	0.00891 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
13q loss	426 (41%)	618	8e-05 (0.0367)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.295 (1.00)	0.0008 (0.278)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
15q loss	312 (30%)	732	4e-05 (0.0196)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.00197 (0.585)	0.00589 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
17q gain	217 (21%)	827	1e-05 (0.0096)	7e-05 (0.0326)	1e-05 (0.0096)	5e-05 (0.0238)	0.566 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.0355 (1.00)	1e-05 (0.0096)	0.281 (1.00)	2e-05 (0.0107)
2p loss	177 (17%)	867	0.00605 (1.00)	0.0145 (1.00)	1e-05 (0.0096)	0.00048 (0.182)	0.00049 (0.185)	0.00027 (0.107)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	8e-05 (0.0367)	0.00455 (1.00)	0.00025 (0.101)
11p loss	267 (26%)	777	0.0107 (1.00)	0.015 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.0148 (1.00)	0.00065 (0.235)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)	0.00012 (0.0522)	0.00016 (0.0683)
18q loss	312 (30%)	732	0.00027 (0.107)	0.00021 (0.0865)	1e-05 (0.0096)	1e-05 (0.0096)	0.0503 (1.00)	0.107 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00257 (0.735)	3e-05 (0.0152)	0.00069 (0.248)	0.00026 (0.104)
19q loss	156 (15%)	888	0.0041 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.12 (1.00)	0.00357 (0.978)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
20p loss	88 (8%)	956	0.00284 (0.801)	0.0001 (0.0447)	1e-05 (0.0096)	1e-05 (0.0096)	0.11 (1.00)	0.175 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)
5q gain	204 (20%)	840	0.00433 (1.00)	0.00242 (0.699)	1e-05 (0.0096)	0.00046 (0.176)	0.00136 (0.438)	9e-05 (0.0409)	0.00078 (0.274)	0.00051 (0.191)	0.00034 (0.133)	4e-05 (0.0196)	0.00037 (0.144)	0.00039 (0.151)
12p gain	225 (22%)	819	0.00146 (0.463)	0.0001 (0.0447)	1e-05 (0.0096)	0.00121 (0.398)	0.102 (1.00)	0.018 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	5e-05 (0.0238)	1e-05 (0.0096)	0.00016 (0.0683)	0.00018 (0.076)
20p gain	403 (39%)	641	0.0001 (0.0447)	4e-05 (0.0196)	1e-05 (0.0096)	0.0035 (0.963)	0.00656 (1.00)	0.276 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00032 (0.126)	1e-05 (0.0096)	0.00141 (0.451)	1e-05 (0.0096)
xq gain	134 (13%)	910	0.00066 (0.238)	0.00137 (0.44)	1e-05 (0.0096)	6e-05 (0.0282)	0.561 (1.00)	0.249 (1.00)	2e-05 (0.0107)	1e-05 (0.0096)	1e-05 (0.0096)	0.00014 (0.0605)	0.00011 (0.0484)	0.00111 (0.371)
7p loss	107 (10%)	937	0.0207 (1.00)	0.00108 (0.363)	1e-05 (0.0096)	0.00036 (0.141)	0.143 (1.00)	0.0325 (1.00)	7e-05 (0.0326)	8e-05 (0.0367)	1e-05 (0.0096)	0.00021 (0.0865)	4e-05 (0.0196)	0.00058 (0.215)
10q loss	225 (22%)	819	0.00267 (0.758)	0.00636 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00149 (0.466)	0.0378 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	6e-05 (0.0282)	1e-05 (0.0096)
12p loss	145 (14%)	899	0.00233 (0.683)	0.00097 (0.33)	1e-05 (0.0096)	1e-05 (0.0096)	0.0203 (1.00)	0.00729 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	2e-05 (0.0107)	2e-05 (0.0107)
20q loss	50 (5%)	994	0.0121 (1.00)	0.00567 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.138 (1.00)	0.0403 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	3e-05 (0.0152)	1e-05 (0.0096)	2e-05 (0.0107)	1e-05 (0.0096)
10q gain	119 (11%)	925	0.0503 (1.00)	0.00158 (0.487)	1e-05 (0.0096)	0.00313 (0.873)	0.0371 (1.00)	0.039 (1.00)	7e-05 (0.0326)	1e-05 (0.0096)	0.00063 (0.229)	1e-05 (0.0096)	0.00029 (0.115)	0.0001 (0.0447)
11q gain	92 (9%)	952	0.243 (1.00)	0.0777 (1.00)	1e-05 (0.0096)	0.0006 (0.221)	0.929 (1.00)	0.732 (1.00)	0.00189 (0.565)	7e-05 (0.0326)	1e-05 (0.0096)	1e-05 (0.0096)	4e-05 (0.0196)	1e-05 (0.0096)
1p loss	237 (23%)	807	0.00061 (0.224)	1e-05 (0.0096)	1e-05 (0.0096)	1e-05 (0.0096)	0.499 (1.00)	0.439 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00643 (1.00)	1e-05 (0.0096)	0.395 (1.00)	0.00072 (0.258)
11q loss	354 (34%)	690	0.00014 (0.0605)	4e-05 (0.0196)	1e-05 (0.0096)	0.00011 (0.0484)	0.798 (1.00)	0.00429 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.236 (1.00)	0.00046 (0.176)	0.0971 (1.00)	0.00834 (1.00)
18p loss	310 (30%)	734	0.00023 (0.0934)	0.00037 (0.144)	1e-05 (0.0096)	1e-05 (0.0096)	0.212 (1.00)	0.277 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.0093 (1.00)	2e-05 (0.0107)	0.0167 (1.00)	0.00148 (0.466)
3p gain	136 (13%)	908	0.0247 (1.00)	0.0346 (1.00)	1e-05 (0.0096)	7e-05 (0.0326)	0.429 (1.00)	0.0574 (1.00)	9e-05 (0.0409)	1e-05 (0.0096)	0.00073 (0.259)	3e-05 (0.0152)	0.00309 (0.865)	0.00018 (0.076)
7q gain	254 (24%)	790	0.00102 (0.345)	0.01 (1.00)	1e-05 (0.0096)	3e-05 (0.0152)	0.032 (1.00)	0.179 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.00062 (0.227)	3e-05 (0.0152)	0.0233 (1.00)	0.00578 (1.00)
11p gain	135 (13%)	909	0.75 (1.00)	0.0979 (1.00)	1e-05 (0.0096)	0.00262 (0.747)	0.984 (1.00)	0.497 (1.00)	0.00725 (1.00)	0.00011 (0.0484)	5e-05 (0.0238)	0.0002 (0.0826)	0.00026 (0.104)	4e-05 (0.0196)
2q loss	201 (19%)	843	0.0588 (1.00)	0.0421 (1.00)	1e-05 (0.0096)	0.0423 (1.00)	9e-05 (0.0409)	0.00033 (0.13)	0.00092 (0.316)	1e-05 (0.0096)	0.00018 (0.076)	0.00058 (0.215)	0.00761 (1.00)	0.00159 (0.488)
4q gain	71 (7%)	973	3e-05 (0.0152)	0.00025 (0.101)	1e-05 (0.0096)	0.013 (1.00)	0.242 (1.00)	0.0236 (1.00)	3e-05 (0.0152)	2e-05 (0.0107)	0.345 (1.00)	0.221 (1.00)	0.22 (1.00)	0.0215 (1.00)
14q gain	139 (13%)	905	0.00123 (0.403)	0.0152 (1.00)	1e-05 (0.0096)	0.00126 (0.412)	0.496 (1.00)	0.235 (1.00)	4e-05 (0.0196)	4e-05 (0.0196)	0.00155 (0.479)	1e-05 (0.0096)	0.0147 (1.00)	0.00013 (0.0564)
19p gain	178 (17%)	866	0.00294 (0.826)	0.0103 (1.00)	1e-05 (0.0096)	0.00633 (1.00)	0.00984 (1.00)	0.0139 (1.00)	3e-05 (0.0152)	4e-05 (0.0196)	2e-05 (0.0107)	3e-05 (0.0152)	0.00319 (0.884)	0.00621 (1.00)
19q gain	210 (20%)	834	0.00521 (1.00)	0.0109 (1.00)	1e-05 (0.0096)	0.00078 (0.274)	0.00867 (1.00)	0.0267 (1.00)	1e-05 (0.0096)	3e-05 (0.0152)	0.0001 (0.0447)	5e-05 (0.0238)	0.00484 (1.00)	0.00668 (1.00)
3q loss	99 (9%)	945	0.00077 (0.271)	0.00015 (0.0643)	1e-05 (0.0096)	0.0015 (0.468)	0.199 (1.00)	0.00769 (1.00)	0.00018 (0.076)	1e-05 (0.0096)	0.00017 (0.0719)	0.00074 (0.262)	0.00469 (1.00)	0.0141 (1.00)
6q loss	263 (25%)	781	0.00062 (0.227)	0.0151 (1.00)	1e-05 (0.0096)	0.00837 (1.00)	0.239 (1.00)	0.0464 (1.00)	2e-05 (0.0107)	1e-05 (0.0096)	0.0186 (1.00)	0.00021 (0.0865)	0.0139 (1.00)	0.00117 (0.387)
xq loss	176 (17%)	868	0.156 (1.00)	0.0027 (0.764)	1e-05 (0.0096)	2e-05 (0.0107)	0.0397 (1.00)	0.0156 (1.00)	3e-05 (0.0152)	1e-05 (0.0096)	1e-05 (0.0096)	0.00134 (0.434)	0.00448 (1.00)	0.00479 (1.00)
4p gain	75 (7%)	969	0.00054 (0.201)	0.00126 (0.412)	1e-05 (0.0096)	0.0288 (1.00)	0.737 (1.00)	0.162 (1.00)	3e-05 (0.0152)	1e-05 (0.0096)	0.317 (1.00)	0.0244 (1.00)	0.344 (1.00)	0.00589 (1.00)
8p gain	282 (27%)	762	0.137 (1.00)	0.174 (1.00)	1e-05 (0.0096)	0.00039 (0.151)	0.784 (1.00)	0.0232 (1.00)	0.0018 (0.54)	0.00021 (0.0865)	0.154 (1.00)	0.0288 (1.00)	0.00046 (0.176)	0.00443 (1.00)
12q gain	189 (18%)	855	0.00235 (0.686)	0.00253 (0.729)	1e-05 (0.0096)	0.00415 (1.00)	0.284 (1.00)	0.109 (1.00)	1e-05 (0.0096)	1e-05 (0.0096)	0.0588 (1.00)	0.00019 (0.0788)	0.15 (1.00)	0.00072 (0.258)
10p loss	168 (16%)	876	0.241 (1.00)	0.196 (1.00)	1e-05 (0.0096)	0.00023 (0.0934)	0.28 (1.00)	0.439 (1.00)	0.00022 (0.0895)	0.00094 (0.321)	0.0327 (1.00)	0.00013 (0.0564)	0.055 (1.00)	0.019 (1.00)
16p loss	165 (16%)	879	0.219 (1.00)	0.0709 (1.00)	0.00026 (0.104)	0.00411 (1.00)	0.0264 (1.00)	0.0473 (1.00)	0.00049 (0.185)	0.00201 (0.593)	8e-05 (0.0367)	0.00099 (0.336)	0.00015 (0.0643)	0.00084 (0.29)
1q gain	683 (65%)	361	0.00111 (0.371)	0.00573 (1.00)	1e-05 (0.0096)	0.0641 (1.00)	0.605 (1.00)	0.293 (1.00)	1e-05 (0.0096)	0.00018 (0.076)	0.53 (1.00)	0.116 (1.00)	0.683 (1.00)	0.329 (1.00)
7p gain	297 (28%)	747	0.00676 (1.00)	0.0801 (1.00)	1e-05 (0.0096)	4e-05 (0.0196)	0.512 (1.00)	0.78 (1.00)	0.00079 (0.276)	0.00048 (0.182)	0.0841 (1.00)	0.00112 (0.372)	0.182 (1.00)	0.00349 (0.963)
16q gain	136 (13%)	908	0.298 (1.00)	0.229 (1.00)	9e-05 (0.0409)	0.00853 (1.00)	0.0924 (1.00)	0.419 (1.00)	0.0845 (1.00)	0.00092 (0.316)	0.00173 (0.522)	0.00045 (0.173)	0.0251 (1.00)	0.0006 (0.221)
7q loss	116 (11%)	928	0.0359 (1.00)	0.00154 (0.477)	2e-05 (0.0107)	0.0464 (1.00)	0.689 (1.00)	0.492 (1.00)	0.00999 (1.00)	0.00135 (0.436)	2e-05 (0.0107)	0.00054 (0.201)	0.0015 (0.468)	0.00656 (1.00)
13q gain	91 (9%)	953	0.219 (1.00)	0.284 (1.00)	4e-05 (0.0196)	0.025 (1.00)	0.0209 (1.00)	0.14 (1.00)	0.0262 (1.00)	0.00141 (0.451)	0.00072 (0.258)	5e-05 (0.0238)	0.043 (1.00)	0.0051 (1.00)
6p loss	181 (17%)	863	0.0428 (1.00)	0.171 (1.00)	1e-05 (0.0096)	0.132 (1.00)	0.677 (1.00)	0.0245 (1.00)	0.00212 (0.623)	0.00501 (1.00)	0.166 (1.00)	0.0269 (1.00)	0.0544 (1.00)	0.00064 (0.232)
21q loss	171 (16%)	873	0.0332 (1.00)	0.151 (1.00)	1e-05 (0.0096)	0.00165 (0.503)	0.805 (1.00)	0.178 (1.00)	0.0552 (1.00)	0.00048 (0.182)	0.00317 (0.881)	0.00846 (1.00)	0.0554 (1.00)	0.00142 (0.452)
22q loss	471 (45%)	573	0.054 (1.00)	0.00568 (1.00)	1e-05 (0.0096)	0.0543 (1.00)	0.0222 (1.00)	0.00088 (0.303)	0.00757 (1.00)	9e-05 (0.0409)	0.0903 (1.00)	0.00199 (0.589)	0.546 (1.00)	0.0352 (1.00)
5p gain	304 (29%)	740	0.0226 (1.00)	0.0311 (1.00)	1e-05 (0.0096)	0.00473 (1.00)	0.925 (1.00)	0.118 (1.00)	0.0797 (1.00)	0.0196 (1.00)	0.18 (1.00)	0.0108 (1.00)	0.0459 (1.00)	0.00647 (1.00)
9q gain	113 (11%)	931	0.175 (1.00)	0.00102 (0.345)	1e-05 (0.0096)	0.102 (1.00)	0.934 (1.00)	0.0822 (1.00)	0.00379 (1.00)	0.0101 (1.00)	0.206 (1.00)	0.0655 (1.00)	0.0508 (1.00)	0.0365 (1.00)
15q gain	85 (8%)	959	0.0417 (1.00)	0.279 (1.00)	0.00363 (0.991)	0.0364 (1.00)	0.49 (1.00)	0.0618 (1.00)	0.0794 (1.00)	0.00117 (0.387)	0.349 (1.00)	0.00039 (0.151)	0.262 (1.00)	0.108 (1.00)
17p gain	106 (10%)	938	0.0567 (1.00)	0.392 (1.00)	1e-05 (0.0096)	0.0276 (1.00)	0.643 (1.00)	0.345 (1.00)	0.0226 (1.00)	0.00174 (0.524)	0.313 (1.00)	0.285 (1.00)	0.761 (1.00)	0.21 (1.00)
1q loss	52 (5%)	992	0.0745 (1.00)	0.00239 (0.693)	0.00011 (0.0484)	0.282 (1.00)	0.334 (1.00)	0.177 (1.00)	0.00236 (0.687)	0.00163 (0.499)	0.00253 (0.729)	0.0236 (1.00)	0.497 (1.00)	0.502 (1.00)
8q loss	89 (9%)	955	0.0269 (1.00)	0.146 (1.00)	0.015 (1.00)	0.0649 (1.00)	0.794 (1.00)	0.128 (1.00)	0.0856 (1.00)	0.114 (1.00)	0.619 (1.00)	0.803 (1.00)	0.305 (1.00)	0.352 (1.00)

'1p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S1. Gene #1: '1p gain' 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
1P GAIN MUTATED	2	3	17	40	7	18	6	5
1P GAIN WILD-TYPE	19	33	102	56	102	54	14	35

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S2. Gene #1: '1p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
1P GAIN MUTATED	14	16	26	36	6
1P GAIN WILD-TYPE	87	136	88	52	52

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

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
1P GAIN MUTATED	44	32	9	106	9
1P GAIN WILD-TYPE	355	208	90	158	33

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S4. Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
1P GAIN MUTATED	53	22	28	9	29
1P GAIN WILD-TYPE	79	175	149	79	99

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

'1p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S5. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
1P GAIN MUTATED	50	17	13
1P GAIN WILD-TYPE	99	115	104

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S6. Gene #1: '1p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
1P GAIN MUTATED	4	12	30	25	9
1P GAIN WILD-TYPE	60	94	60	82	22

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S7. Gene #1: '1p gain' 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
1P GAIN MUTATED	81	19	20	37	33	6	3
1P GAIN WILD-TYPE	109	124	214	124	211	46	13

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S8. Gene #1: '1p gain' 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
1P GAIN MUTATED	76	33	15	36	22	17
1P GAIN WILD-TYPE	102	210	182	144	162	41

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S9. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
1P GAIN MUTATED	41	52	104
1P GAIN WILD-TYPE	265	370	193

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S10. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
1P GAIN MUTATED	19	21	58	56	43
1P GAIN WILD-TYPE	155	165	347	78	83

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S11. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
1P GAIN MUTATED	32	33	74
1P GAIN WILD-TYPE	217	223	135

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S12. Gene #1: '1p gain' 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
1P GAIN MUTATED	54	7	27	22	11	18
1P GAIN WILD-TYPE	73	60	166	113	114	49

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
1Q GAIN MUTATED	236	155	95	170	27
1Q GAIN WILD-TYPE	163	85	4	94	15

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S14. Gene #2: '1q gain' 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
1Q GAIN MUTATED	125	86	187	109	127	37	9
1Q GAIN WILD-TYPE	65	57	47	52	117	15	7

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S15. Gene #2: '1q gain' 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
1Q GAIN MUTATED	119	157	143	131	96	34
1Q GAIN WILD-TYPE	59	86	54	49	88	24

Figure S15. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S16. Gene #3: '2p gain' 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
2P GAIN MUTATED	1	1	6	31	1	20	1	0
2P GAIN WILD-TYPE	20	35	113	65	108	52	19	40

Figure S16. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S17. Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
2P GAIN MUTATED	5	1	27	27	1
2P GAIN WILD-TYPE	96	151	87	61	57

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S18. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
2P GAIN MUTATED	13	19	7	75	5
2P GAIN WILD-TYPE	386	221	92	189	37

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S19. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
2P GAIN MUTATED	39	2	19	6	13
2P GAIN WILD-TYPE	93	195	158	82	115

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S20. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
2P GAIN MUTATED	40	2	9
2P GAIN WILD-TYPE	109	130	108

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S21. Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2P GAIN MUTATED	1	5	32	8	5
2P GAIN WILD-TYPE	63	101	58	99	26

Figure S21. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S22. Gene #3: '2p gain' 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
2P GAIN MUTATED	59	2	4	41	11	0	2
2P GAIN WILD-TYPE	131	141	230	120	233	52	14

Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S23. Gene #3: '2p gain' 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
2P GAIN MUTATED	56	5	3	26	6	23
2P GAIN WILD-TYPE	122	238	194	154	178	35

Figure S23. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S24. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
2P GAIN MUTATED	7	23	83
2P GAIN WILD-TYPE	299	399	214

Figure S24. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S25. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
2P GAIN MUTATED	3	3	33	39	35
2P GAIN WILD-TYPE	171	183	372	95	91

Figure S25. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S26. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
2P GAIN MUTATED	11	10	61
2P GAIN WILD-TYPE	238	246	148

Figure S26. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S27. Gene #3: '2p gain' 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
2P GAIN MUTATED	38	1	19	5	1	18
2P GAIN WILD-TYPE	89	66	174	130	124	49

Figure S27. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S28. Gene #4: '2q gain' 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
2Q GAIN MUTATED	1	1	5	18	1	14	0	0
2Q GAIN WILD-TYPE	20	35	114	78	108	58	20	40

Figure S28. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S29. Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
2Q GAIN MUTATED	4	1	18	16	1
2Q GAIN WILD-TYPE	97	151	96	72	57

Figure S29. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S30. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
2Q GAIN MUTATED	10	11	6	45	1
2Q GAIN WILD-TYPE	389	229	93	219	41

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S31. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
2Q GAIN MUTATED	23	1	12	3	4
2Q GAIN WILD-TYPE	109	196	165	85	124

Figure S31. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S32. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
2Q GAIN MUTATED	26	2	4
2Q GAIN WILD-TYPE	123	130	113

Figure S32. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S33. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2Q GAIN MUTATED	1	3	19	5	4
2Q GAIN WILD-TYPE	63	103	71	102	27

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S34. Gene #4: '2q gain' 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
2Q GAIN MUTATED	34	2	4	28	5	0	0
2Q GAIN WILD-TYPE	156	141	230	133	239	52	16

Figure S34. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S35. Gene #4: '2q gain' 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
2Q GAIN MUTATED	33	3	3	19	3	12
2Q GAIN WILD-TYPE	145	240	194	161	181	46

Figure S35. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S36. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
2Q GAIN MUTATED	5	16	47
2Q GAIN WILD-TYPE	301	406	250

Figure S36. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S37. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
2Q GAIN MUTATED	3	1	22	17	25
2Q GAIN WILD-TYPE	171	185	383	117	101

Figure S37. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S38. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
2Q GAIN MUTATED	7	9	37
2Q GAIN WILD-TYPE	242	247	172

Figure S38. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S39. Gene #4: '2q gain' 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
2Q GAIN MUTATED	24	1	15	1	1	11
2Q GAIN WILD-TYPE	103	66	178	134	124	56

Figure S39. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S40. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
3P GAIN MUTATED	12	47	21	47	9
3P GAIN WILD-TYPE	387	193	78	217	33

Figure S40. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S41. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
3P GAIN MUTATED	30	15	20	6	7
3P GAIN WILD-TYPE	102	182	157	82	121

Figure S41. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S42. Gene #5: '3p gain' 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
3P GAIN MUTATED	39	7	28	19	37	1	4
3P GAIN WILD-TYPE	151	136	206	142	207	51	12

Figure S42. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S43. Gene #5: '3p gain' 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
3P GAIN MUTATED	38	12	18	28	32	7
3P GAIN WILD-TYPE	140	231	179	152	152	51

Figure S43. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S44. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
3P GAIN MUTATED	7	18	54	29	24
3P GAIN WILD-TYPE	167	168	351	105	102

Figure S44. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S45. Gene #5: '3p gain' 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
3P GAIN MUTATED	28	3	22	18	5	8
3P GAIN WILD-TYPE	99	64	171	117	120	59

Figure S45. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S46. Gene #6: '3q gain' 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
3Q GAIN MUTATED	2	7	29	32	16	17	7	1
3Q GAIN WILD-TYPE	19	29	90	64	93	55	13	39

Figure S46. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S47. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
3Q GAIN MUTATED	21	16	33	29	12
3Q GAIN WILD-TYPE	80	136	81	59	46

Figure S47. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S48. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
3Q GAIN MUTATED	21	59	25	94	9
3Q GAIN WILD-TYPE	378	181	74	170	33

Figure S48. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S49. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
3Q GAIN MUTATED	52	19	34	10	11
3Q GAIN WILD-TYPE	80	178	143	78	117

Figure S49. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S50. Gene #6: '3q gain' 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
3Q GAIN MUTATED	75	9	34	34	49	1	5
3Q GAIN WILD-TYPE	115	134	200	127	195	51	11

Figure S50. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S51. Gene #6: '3q gain' 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
3Q GAIN MUTATED	72	18	21	44	40	12
3Q GAIN WILD-TYPE	106	225	176	136	144	46

Figure S51. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S52. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
3Q GAIN MUTATED	32	70	102
3Q GAIN WILD-TYPE	274	352	195

Figure S52. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S53. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
3Q GAIN MUTATED	10	29	73	54	38
3Q GAIN WILD-TYPE	164	157	332	80	88

Figure S53. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S54. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
3Q GAIN MUTATED	34	32	73
3Q GAIN WILD-TYPE	215	224	136

Figure S54. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S55. Gene #6: '3q gain' 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
3Q GAIN MUTATED	58	4	28	26	9	14
3Q GAIN WILD-TYPE	69	63	165	109	116	53

Figure S55. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.2

Table S56. Gene #7: '4p gain' 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
4P GAIN MUTATED	1	2	22	3	3	4	0	2
4P GAIN WILD-TYPE	20	34	97	93	106	68	20	38

Figure S56. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S57. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
4P GAIN MUTATED	6	45	3	17	4
4P GAIN WILD-TYPE	393	195	96	247	38

Figure S57. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S58. Gene #7: '4p gain' 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
4P GAIN MUTATED	9	6	10	10	39	1	0
4P GAIN WILD-TYPE	181	137	224	151	205	51	16

Figure S58. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S59. Gene #7: '4p gain' 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
4P GAIN MUTATED	7	11	7	18	29	3
4P GAIN WILD-TYPE	171	232	190	162	155	55

Figure S59. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MRNA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S60. Gene #8: '4q gain' 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
4Q GAIN MUTATED	1	2	23	2	3	2	0	2
4Q GAIN WILD-TYPE	20	34	96	94	106	70	20	38

Figure S60. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.1

Table S61. Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
4Q GAIN MUTATED	18	8	6	2	1
4Q GAIN WILD-TYPE	83	144	108	86	57

Figure S61. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S62. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
4Q GAIN MUTATED	5	44	2	14	6
4Q GAIN WILD-TYPE	394	196	97	250	36

Figure S62. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S63. Gene #8: '4q gain' 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
4Q GAIN MUTATED	9	5	10	8	38	1	0
4Q GAIN WILD-TYPE	181	138	224	153	206	51	16

Figure S63. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S64. Gene #8: '4q gain' 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
4Q GAIN MUTATED	8	10	6	13	31	3
4Q GAIN WILD-TYPE	170	233	191	167	153	55

Figure S64. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S65. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
5P GAIN MUTATED	57	108	51	77	11
5P GAIN WILD-TYPE	342	132	48	187	31

Figure S65. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S66. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
5Q GAIN MUTATED	47	80	48	20	9
5Q GAIN WILD-TYPE	352	160	51	244	33

Figure S66. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S67. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
5Q GAIN MUTATED	16	50	44	17	13
5Q GAIN WILD-TYPE	116	147	133	71	115

Figure S67. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S68. Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
5Q GAIN MUTATED	22	23	5	24	7
5Q GAIN WILD-TYPE	42	83	85	83	24

Figure S68. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.19

Table S69. Gene #10: '5q gain' 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
5Q GAIN MUTATED	16	50	42	40	47	8
5Q GAIN WILD-TYPE	162	193	155	140	137	50

Figure S69. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.13

Table S70. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
5Q GAIN MUTATED	66	99	36
5Q GAIN WILD-TYPE	240	323	261

Figure S70. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S71. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
5Q GAIN MUTATED	29	41	101	9	21
5Q GAIN WILD-TYPE	145	145	304	125	105

Figure S71. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.14

Table S72. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
5Q GAIN MUTATED	65	51	24
5Q GAIN WILD-TYPE	184	205	185

Figure S72. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S73. Gene #10: '5q gain' 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
5Q GAIN MUTATED	12	13	57	28	20	10
5Q GAIN WILD-TYPE	115	54	136	107	105	57

Figure S73. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S74. Gene #11: '6p gain' 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
6P GAIN MUTATED	2	2	18	36	13	19	7	2
6P GAIN WILD-TYPE	19	34	101	60	96	53	13	38

Figure S74. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S75. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
6P GAIN MUTATED	15	13	34	31	6
6P GAIN WILD-TYPE	86	139	80	57	52

Figure S75. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S76. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
6P GAIN MUTATED	17	42	21	112	9
6P GAIN WILD-TYPE	382	198	78	152	33

Figure S76. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S77. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
6P GAIN MUTATED	58	19	41	5	13
6P GAIN WILD-TYPE	74	178	136	83	115

Figure S77. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.028

Table S78. Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
6P GAIN MUTATED	46	18	14
6P GAIN WILD-TYPE	103	114	103

Figure S78. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S79. Gene #11: '6p gain' 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
6P GAIN MUTATED	83	9	27	35	35	4	7
6P GAIN WILD-TYPE	107	134	207	126	209	48	9

Figure S79. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S80. Gene #11: '6p gain' 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
6P GAIN MUTATED	76	19	14	55	25	11
6P GAIN WILD-TYPE	102	224	183	125	159	47

Figure S80. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S81. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
6P GAIN MUTATED	25	65	103
6P GAIN WILD-TYPE	281	357	194

Figure S81. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S82. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
6P GAIN MUTATED	8	16	70	55	44
6P GAIN WILD-TYPE	166	170	335	79	82

Figure S82. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S83. Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
6P GAIN MUTATED	27	27	78
6P GAIN WILD-TYPE	222	229	131

Figure S83. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S84. Gene #11: '6p gain' 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
6P GAIN MUTATED	56	3	28	20	8	17
6P GAIN WILD-TYPE	71	64	165	115	117	50

Figure S84. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S85. Gene #12: '6q gain' 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
6Q GAIN MUTATED	1	0	9	29	11	13	7	2
6Q GAIN WILD-TYPE	20	36	110	67	98	59	13	38

Figure S85. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S86. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
6Q GAIN MUTATED	9	11	24	24	4
6Q GAIN WILD-TYPE	92	141	90	64	54

Figure S86. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S87. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
6Q GAIN MUTATED	12	20	16	92	6
6Q GAIN WILD-TYPE	387	220	83	172	36

Figure S87. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S88. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
6Q GAIN MUTATED	43	9	28	3	12
6Q GAIN WILD-TYPE	89	188	149	85	116

Figure S88. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S89. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
6Q GAIN MUTATED	39	9	10
6Q GAIN WILD-TYPE	110	123	107

Figure S89. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S90. Gene #12: '6q gain' 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
6Q GAIN MUTATED	63	6	21	24	21	4	6
6Q GAIN WILD-TYPE	127	137	213	137	223	48	10

Figure S90. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S91. Gene #12: '6q gain' 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
6Q GAIN MUTATED	57	13	8	42	18	7
6Q GAIN WILD-TYPE	121	230	189	138	166	51

Figure S91. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S92. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
6Q GAIN MUTATED	17	40	83
6Q GAIN WILD-TYPE	289	382	214

Figure S92. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S93. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
6Q GAIN MUTATED	7	12	46	39	36
6Q GAIN WILD-TYPE	167	174	359	95	90

Figure S93. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S94. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
6Q GAIN MUTATED	20	17	65
6Q GAIN WILD-TYPE	229	239	144

Figure S94. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S95. Gene #12: '6q gain' 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
6Q GAIN MUTATED	46	2	20	11	8	15
6Q GAIN WILD-TYPE	81	65	173	124	117	52

Figure S95. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S96. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
7P GAIN MUTATED	72	69	53	90	13
7P GAIN WILD-TYPE	327	171	46	174	29

Figure S96. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S97. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
7P GAIN MUTATED	52	50	60	23	17
7P GAIN WILD-TYPE	80	147	117	65	111

Figure S97. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.18

Table S98. Gene #13: '7p gain' 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
7P GAIN MUTATED	61	47	51	62	51	24
7P GAIN WILD-TYPE	117	196	146	118	133	34

Figure S98. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S99. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
7Q GAIN MUTATED	56	55	48	84	11
7Q GAIN WILD-TYPE	343	185	51	180	31

Figure S99. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S100. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
7Q GAIN MUTATED	50	44	45	17	14
7Q GAIN WILD-TYPE	82	153	132	71	114

Figure S100. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S101. Gene #14: '7q gain' 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
7Q GAIN MUTATED	71	22	56	46	52	6	0
7Q GAIN WILD-TYPE	119	121	178	115	192	46	16

Figure S101. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S102. Gene #14: '7q gain' 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
7Q GAIN MUTATED	69	35	45	45	41	18
7Q GAIN WILD-TYPE	109	208	152	135	143	40

Figure S102. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.23

Table S103. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
7Q GAIN MUTATED	70	82	95
7Q GAIN WILD-TYPE	236	340	202

Figure S103. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S104. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
7Q GAIN MUTATED	31	30	97	54	35
7Q GAIN WILD-TYPE	143	156	308	80	91

Figure S104. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S105. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
8P GAIN MUTATED	78	65	40	77	22
8P GAIN WILD-TYPE	321	175	59	187	20

Figure S105. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S106. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
8P GAIN MUTATED	53	48	48	23	20
8P GAIN WILD-TYPE	79	149	129	65	108

Figure S106. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.087

Table S107. Gene #15: '8p gain' 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
8P GAIN MUTATED	64	47	46	46	66	12
8P GAIN WILD-TYPE	114	196	151	134	118	46

Figure S107. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S108. Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
8P GAIN MUTATED	60	54	77
8P GAIN WILD-TYPE	189	202	132

Figure S108. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S109. Gene #16: '8q gain' 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
8Q GAIN MUTATED	14	12	74	62	44	35	15	14
8Q GAIN WILD-TYPE	7	24	45	34	65	37	5	26

Figure S109. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S110. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
8Q GAIN MUTATED	65	68	65	56	16
8Q GAIN WILD-TYPE	36	84	49	32	42

Figure S110. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S111. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
8Q GAIN MUTATED	120	146	44	169	37
8Q GAIN WILD-TYPE	279	94	55	95	5

Figure S111. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S112. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
8Q GAIN MUTATED	91	74	92	31	54
8Q GAIN WILD-TYPE	41	123	85	57	74

Figure S112. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S113. Gene #16: '8q gain' 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
8Q GAIN MUTATED	127	54	81	75	149	15	12
8Q GAIN WILD-TYPE	63	89	153	86	95	37	4

Figure S113. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S114. Gene #16: '8q gain' 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
8Q GAIN MUTATED	119	88	60	104	114	28
8Q GAIN WILD-TYPE	59	155	137	76	70	30

Figure S114. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S115. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
8Q GAIN MUTATED	106	211	189
8Q GAIN WILD-TYPE	200	211	108

Figure S115. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S116. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
8Q GAIN MUTATED	48	78	212	93	75
8Q GAIN WILD-TYPE	126	108	193	41	51

Figure S116. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S117. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
8Q GAIN MUTATED	115	86	141
8Q GAIN WILD-TYPE	134	170	68

Figure S117. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S118. Gene #16: '8q gain' 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
8Q GAIN MUTATED	88	16	96	69	33	40
8Q GAIN WILD-TYPE	39	51	97	66	92	27

Figure S118. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S119. Gene #17: '9p gain' 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
9P GAIN MUTATED	1	2	3	33	14	9	0	5
9P GAIN WILD-TYPE	20	34	116	63	95	63	20	35

Figure S119. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S120. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
9P GAIN MUTATED	0	15	13	30	9
9P GAIN WILD-TYPE	101	137	101	58	49

Figure S120. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S121. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
9P GAIN MUTATED	22	13	30	61	8
9P GAIN WILD-TYPE	377	227	69	203	34

Figure S121. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S122. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
9P GAIN MUTATED	35	22	15	6	10
9P GAIN WILD-TYPE	97	175	162	82	118

Figure S122. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S123. Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
9P GAIN MUTATED	9	9	25	4	6
9P GAIN WILD-TYPE	55	97	65	103	25

Figure S123. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S124. Gene #17: '9p gain' 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
9P GAIN MUTATED	57	7	27	21	15	5	2
9P GAIN WILD-TYPE	133	136	207	140	229	47	14

Figure S124. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S125. Gene #17: '9p gain' 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
9P GAIN MUTATED	54	16	21	24	14	5
9P GAIN WILD-TYPE	124	227	176	156	170	53

Figure S125. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S126. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
9P GAIN MUTATED	28	37	66
9P GAIN WILD-TYPE	278	385	231

Figure S126. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S127. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
9P GAIN MUTATED	13	12	50	41	15
9P GAIN WILD-TYPE	161	174	355	93	111

Figure S127. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.068

Table S128. Gene #17: '9p gain' 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
9P GAIN MUTATED	33	10	26	12	8	6
9P GAIN WILD-TYPE	94	57	167	123	117	61

Figure S128. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S129. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
9Q GAIN MUTATED	23	16	30	39	5
9Q GAIN WILD-TYPE	376	224	69	225	37

Figure S129. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S130. Gene #19: '10p gain' 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
10P GAIN MUTATED	2	4	17	42	11	26	6	4
10P GAIN WILD-TYPE	19	32	102	54	98	46	14	36

Figure S130. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S131. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
10P GAIN MUTATED	10	18	40	39	5
10P GAIN WILD-TYPE	91	134	74	49	53

Figure S131. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S132. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
10P GAIN MUTATED	22	44	18	113	8
10P GAIN WILD-TYPE	377	196	81	151	34

Figure S132. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S133. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
10P GAIN MUTATED	59	13	34	5	22
10P GAIN WILD-TYPE	73	184	143	83	106

Figure S133. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S134. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
10P GAIN MUTATED	52	17	20
10P GAIN WILD-TYPE	97	115	97

Figure S134. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S135. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
10P GAIN MUTATED	7	18	40	19	5
10P GAIN WILD-TYPE	57	88	50	88	26

Figure S135. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S136. Gene #19: '10p gain' 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
10P GAIN MUTATED	78	13	22	43	39	4	6
10P GAIN WILD-TYPE	112	130	212	118	205	48	10

Figure S136. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S137. Gene #19: '10p gain' 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
10P GAIN MUTATED	77	21	12	48	28	19
10P GAIN WILD-TYPE	101	222	185	132	156	39

Figure S137. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S138. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
10P GAIN MUTATED	33	61	107
10P GAIN WILD-TYPE	273	361	190

Figure S138. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S139. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
10P GAIN MUTATED	12	14	77	57	41
10P GAIN WILD-TYPE	162	172	328	77	85

Figure S139. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S140. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
10P GAIN MUTATED	33	26	75
10P GAIN WILD-TYPE	216	230	134

Figure S140. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S141. Gene #19: '10p gain' 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
10P GAIN MUTATED	53	5	31	16	8	21
10P GAIN WILD-TYPE	74	62	162	119	117	46

Figure S141. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S142. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
10Q GAIN MUTATED	15	29	16	54	5
10Q GAIN WILD-TYPE	384	211	83	210	37

Figure S142. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S143. Gene #20: '10q gain' 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
10Q GAIN MUTATED	29	10	17	27	27	2	7
10Q GAIN WILD-TYPE	161	133	217	134	217	50	9

Figure S143. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S144. Gene #20: '10q gain' 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
10Q GAIN MUTATED	29	12	10	35	20	13
10Q GAIN WILD-TYPE	149	231	187	145	164	45

Figure S144. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.23

Table S145. Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
10Q GAIN MUTATED	22	44	51
10Q GAIN WILD-TYPE	284	378	246

Figure S145. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S146. Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
10Q GAIN MUTATED	10	7	53	24	23
10Q GAIN WILD-TYPE	164	179	352	110	103

Figure S146. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.11

Table S147. Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
10Q GAIN MUTATED	24	17	38
10Q GAIN WILD-TYPE	225	239	171

Figure S147. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S148. Gene #20: '10q gain' 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
10Q GAIN MUTATED	19	4	25	11	4	16
10Q GAIN WILD-TYPE	108	63	168	124	121	51

Figure S148. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S149. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
11P GAIN MUTATED	20	41	15	53	6
11P GAIN WILD-TYPE	379	199	84	211	36

Figure S149. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.048

Table S150. Gene #21: '11p gain' 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
11P GAIN MUTATED	34	21	11	32	30	7
11P GAIN WILD-TYPE	144	222	186	148	154	51

Figure S150. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S151. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
11P GAIN MUTATED	19	62	52
11P GAIN WILD-TYPE	287	360	245

Figure S151. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.083

Table S152. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
11P GAIN MUTATED	7	23	56	24	23
11P GAIN WILD-TYPE	167	163	349	110	103

Figure S152. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S153. Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
11P GAIN MUTATED	40	16	35
11P GAIN WILD-TYPE	209	240	174

Figure S153. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S154. Gene #21: '11p gain' 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
11P GAIN MUTATED	27	5	35	12	4	8
11P GAIN WILD-TYPE	100	62	158	123	121	59

Figure S154. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S155. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
11Q GAIN MUTATED	11	18	10	47	6
11Q GAIN WILD-TYPE	388	222	89	217	36

Figure S155. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.22

Table S156. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
11Q GAIN MUTATED	25	16	10	5	6
11Q GAIN WILD-TYPE	107	181	167	83	122

Figure S156. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S157. Gene #22: '11q gain' 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
11Q GAIN MUTATED	27	10	11	23	12	9
11Q GAIN WILD-TYPE	151	233	186	157	172	49

Figure S157. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S158. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
11Q GAIN MUTATED	12	31	46
11Q GAIN WILD-TYPE	294	391	251

Figure S158. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S159. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
11Q GAIN MUTATED	3	17	29	20	20
11Q GAIN WILD-TYPE	171	169	376	114	106

Figure S159. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S160. Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
11Q GAIN MUTATED	19	10	33
11Q GAIN WILD-TYPE	230	246	176

Figure S160. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S161. Gene #22: '11q gain' 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
11Q GAIN MUTATED	23	4	15	11	0	9
11Q GAIN WILD-TYPE	104	63	178	124	125	58

Figure S161. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S162. Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
12P GAIN MUTATED	27	17	33	29	9
12P GAIN WILD-TYPE	74	135	81	59	49

Figure S162. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S163. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
12P GAIN MUTATED	18	85	27	84	11
12P GAIN WILD-TYPE	381	155	72	180	31

Figure S163. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S164. Gene #23: '12p gain' 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
12P GAIN MUTATED	60	15	32	45	67	4	2
12P GAIN WILD-TYPE	130	128	202	116	177	48	14

Figure S164. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S165. Gene #23: '12p gain' 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
12P GAIN MUTATED	57	31	20	55	50	12
12P GAIN WILD-TYPE	121	212	177	125	134	46

Figure S165. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S166. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
12P GAIN MUTATED	46	82	90
12P GAIN WILD-TYPE	260	340	207

Figure S166. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S167. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
12P GAIN MUTATED	16	29	95	45	33
12P GAIN WILD-TYPE	158	157	310	89	93

Figure S167. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.068

Table S168. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
12P GAIN MUTATED	49	38	64
12P GAIN WILD-TYPE	200	218	145

Figure S168. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S169. Gene #23: '12p gain' 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
12P GAIN MUTATED	39	6	46	29	13	18
12P GAIN WILD-TYPE	88	61	147	106	112	49

Figure S169. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S170. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
12Q GAIN MUTATED	19	93	26	42	9
12Q GAIN WILD-TYPE	380	147	73	222	33

Figure S170. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S171. Gene #24: '12q gain' 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
12Q GAIN MUTATED	23	15	34	44	66	5	1
12Q GAIN WILD-TYPE	167	128	200	117	178	47	15

Figure S171. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S172. Gene #24: '12q gain' 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
12Q GAIN MUTATED	22	29	26	52	50	9
12Q GAIN WILD-TYPE	156	214	171	128	134	49

Figure S172. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.079

Table S173. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
12Q GAIN MUTATED	15	33	96	17	23
12Q GAIN WILD-TYPE	159	153	309	117	103

Figure S173. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S174. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
13Q GAIN MUTATED	15	25	8	39	4
13Q GAIN WILD-TYPE	384	215	91	225	38

Figure S174. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S175. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
13Q GAIN MUTATED	5	7	41	14	22
13Q GAIN WILD-TYPE	169	179	364	120	104

Figure S175. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S176. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
14Q GAIN MUTATED	27	55	23	27	7
14Q GAIN WILD-TYPE	372	185	76	237	35

Figure S176. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S177. Gene #26: '14q gain' 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
14Q GAIN MUTATED	12	12	38	36	36	2	2
14Q GAIN WILD-TYPE	178	131	196	125	208	50	14

Figure S177. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S178. Gene #26: '14q gain' 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
14Q GAIN MUTATED	11	20	28	35	30	14
14Q GAIN WILD-TYPE	167	223	169	145	154	44

Figure S178. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S179. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
14Q GAIN MUTATED	14	16	81	4	23
14Q GAIN WILD-TYPE	160	170	324	130	103

Figure S179. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.056

Table S180. Gene #26: '14q gain' 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
14Q GAIN MUTATED	10	4	43	18	8	12
14Q GAIN WILD-TYPE	117	63	150	117	117	55

Figure S180. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 0.15

Table S181. Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
15Q GAIN MUTATED	4	10	37	14	19
15Q GAIN WILD-TYPE	170	176	368	120	107

Figure S181. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.079

Table S182. Gene #28: '16p gain' 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
16P GAIN MUTATED	11	14	52	34	73	34	12	14
16P GAIN WILD-TYPE	10	22	67	62	36	38	8	26

Figure S182. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S183. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
16P GAIN MUTATED	151	116	74	98	19
16P GAIN WILD-TYPE	248	124	25	166	23

Figure S183. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S184. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
16P GAIN MUTATED	43	101	85	33	32
16P GAIN WILD-TYPE	89	96	92	55	96

Figure S184. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S185. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
16P GAIN MUTATED	49	54	31	44	11
16P GAIN WILD-TYPE	15	52	59	63	20

Figure S185. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S186. Gene #28: '16p gain' 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
16P GAIN MUTATED	51	57	146	74	98	24	7
16P GAIN WILD-TYPE	139	86	88	87	146	28	9

Figure S186. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S187. Gene #28: '16p gain' 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
16P GAIN MUTATED	47	97	114	85	89	25
16P GAIN WILD-TYPE	131	146	83	95	95	33

Figure S187. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S188. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
16P GAIN MUTATED	139	210	98
16P GAIN WILD-TYPE	167	212	199

Figure S188. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S189. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
16P GAIN MUTATED	75	82	202	31	57
16P GAIN WILD-TYPE	99	104	203	103	69

Figure S189. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.037

Table S190. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
16P GAIN MUTATED	123	117	63
16P GAIN WILD-TYPE	126	139	146

Figure S190. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S191. Gene #28: '16p gain' 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
16P GAIN MUTATED	31	25	101	62	54	30
16P GAIN WILD-TYPE	96	42	92	73	71	37

Figure S191. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S192. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
16Q GAIN MUTATED	28	39	13	49	7
16Q GAIN WILD-TYPE	371	201	86	215	35

Figure S192. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.17

Table S193. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
16Q GAIN MUTATED	11	22	51	17	31
16Q GAIN WILD-TYPE	163	164	354	117	95

Figure S193. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.22

Table S194. Gene #29: '16q gain' 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
16Q GAIN MUTATED	24	4	23	17	8	18
16Q GAIN WILD-TYPE	103	63	170	118	117	49

Figure S194. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S195. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
17P GAIN MUTATED	20	47	11	22	6
17P GAIN WILD-TYPE	379	193	88	242	36

Figure S195. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S196. Gene #31: '17q gain' 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
17Q GAIN MUTATED	4	8	47	9	10	12	5	5
17Q GAIN WILD-TYPE	17	28	72	87	99	60	15	35

Figure S196. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S197. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
17Q GAIN MUTATED	35	24	26	8	7
17Q GAIN WILD-TYPE	66	128	88	80	51

Figure S197. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S198. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
17Q GAIN MUTATED	37	113	19	35	13
17Q GAIN WILD-TYPE	362	127	80	229	29

Figure S198. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S199. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
17Q GAIN MUTATED	16	41	61	15	22
17Q GAIN WILD-TYPE	116	156	116	73	106

Figure S199. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S200. Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
17Q GAIN MUTATED	6	21	8	39	4
17Q GAIN WILD-TYPE	58	85	82	68	27

Figure S200. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S201. Gene #31: '17q gain' 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
17Q GAIN MUTATED	21	24	29	31	97	7	7
17Q GAIN WILD-TYPE	169	119	205	130	147	45	9

Figure S201. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S202. Gene #31: '17q gain' 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
17Q GAIN MUTATED	18	35	24	48	84	7
17Q GAIN WILD-TYPE	160	208	173	132	100	51

Figure S202. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S203. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
17Q GAIN MUTATED	20	47	107	12	26
17Q GAIN WILD-TYPE	154	139	298	122	100

Figure S203. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S204. Gene #31: '17q gain' 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
17Q GAIN MUTATED	17	14	47	50	13	14
17Q GAIN WILD-TYPE	110	53	146	85	112	53

Figure S204. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S205. Gene #32: '18p gain' 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
18P GAIN MUTATED	1	1	19	35	16	10	4	1
18P GAIN WILD-TYPE	20	35	100	61	93	62	16	39

Figure S205. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S206. Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18P GAIN MUTATED	20	13	17	32	5
18P GAIN WILD-TYPE	81	139	97	56	53

Figure S206. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S207. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
18P GAIN MUTATED	18	40	21	83	10
18P GAIN WILD-TYPE	381	200	78	181	32

Figure S207. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S208. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18P GAIN MUTATED	52	21	15	6	13
18P GAIN WILD-TYPE	80	176	162	82	115

Figure S208. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S209. Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
18P GAIN MUTATED	13	9	34	10	4
18P GAIN WILD-TYPE	51	97	56	97	27

Figure S209. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S210. Gene #32: '18p gain' 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
18P GAIN MUTATED	73	6	35	20	35	0	3
18P GAIN WILD-TYPE	117	137	199	141	209	52	13

Figure S210. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S211. Gene #32: '18p gain' 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
18P GAIN MUTATED	70	5	25	24	34	14
18P GAIN WILD-TYPE	108	238	172	156	150	44

Figure S211. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S212. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
18P GAIN MUTATED	27	48	90
18P GAIN WILD-TYPE	279	374	207

Figure S212. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S213. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
18P GAIN MUTATED	10	18	49	54	34
18P GAIN WILD-TYPE	164	168	356	80	92

Figure S213. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S214. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
18P GAIN MUTATED	30	21	68
18P GAIN WILD-TYPE	219	235	141

Figure S214. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S215. Gene #32: '18p gain' 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
18P GAIN MUTATED	51	4	28	19	3	14
18P GAIN WILD-TYPE	76	63	165	116	122	53

Figure S215. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S216. Gene #33: '18q gain' 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
18Q GAIN MUTATED	2	1	21	29	17	5	4	1
18Q GAIN WILD-TYPE	19	35	98	67	92	67	16	39

Figure S216. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.068

Table S217. Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18Q GAIN MUTATED	22	13	14	26	5
18Q GAIN WILD-TYPE	79	139	100	62	53

Figure S217. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S218. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
18Q GAIN MUTATED	15	36	22	64	10
18Q GAIN WILD-TYPE	384	204	77	200	32

Figure S218. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S219. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18Q GAIN MUTATED	33	23	15	6	11
18Q GAIN WILD-TYPE	99	174	162	82	117

Figure S219. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S220. Gene #33: '18q gain' 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
18Q GAIN MUTATED	53	6	36	10	38	1	3
18Q GAIN WILD-TYPE	137	137	198	151	206	51	13

Figure S220. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S221. Gene #33: '18q gain' 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
18Q GAIN MUTATED	51	8	24	20	38	6
18Q GAIN WILD-TYPE	127	235	173	160	146	52

Figure S221. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S222. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
18Q GAIN MUTATED	25	49	67
18Q GAIN WILD-TYPE	281	373	230

Figure S222. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S223. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
18Q GAIN MUTATED	10	20	52	38	21
18Q GAIN WILD-TYPE	164	166	353	96	105

Figure S223. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S224. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
18Q GAIN MUTATED	27	21	46
18Q GAIN WILD-TYPE	222	235	163

Figure S224. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S225. Gene #33: '18q gain' 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
18Q GAIN MUTATED	32	4	28	21	3	6
18Q GAIN WILD-TYPE	95	63	165	114	122	61

Figure S225. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S226. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
19P GAIN MUTATED	31	37	29	75	6
19P GAIN WILD-TYPE	368	203	70	189	36

Figure S226. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S227. Gene #34: '19p gain' 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
19P GAIN MUTATED	59	19	30	30	30	5	4
19P GAIN WILD-TYPE	131	124	204	131	214	47	12

Figure S227. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S228. Gene #34: '19p gain' 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
19P GAIN MUTATED	54	37	21	26	26	13
19P GAIN WILD-TYPE	124	206	176	154	158	45

Figure S228. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S229. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
19P GAIN MUTATED	44	53	78
19P GAIN WILD-TYPE	262	369	219

Figure S229. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S230. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
19P GAIN MUTATED	24	17	65	39	30
19P GAIN WILD-TYPE	150	169	340	95	96

Figure S230. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S231. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
19Q GAIN MUTATED	35	49	31	85	10
19Q GAIN WILD-TYPE	364	191	68	179	32

Figure S231. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S232. Gene #35: '19q gain' 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
19Q GAIN MUTATED	64	23	31	37	45	5	4
19Q GAIN WILD-TYPE	126	120	203	124	199	47	12

Figure S232. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S233. Gene #35: '19q gain' 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
19Q GAIN MUTATED	59	39	22	35	38	16
19Q GAIN WILD-TYPE	119	204	175	145	146	42

Figure S233. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S234. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
19Q GAIN MUTATED	51	71	86
19Q GAIN WILD-TYPE	255	351	211

Figure S234. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S235. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
19Q GAIN MUTATED	27	22	80	39	40
19Q GAIN WILD-TYPE	147	164	325	95	86

Figure S235. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S236. Gene #36: '20p gain' 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
20P GAIN MUTATED	8	13	49	42	34	41	14	7
20P GAIN WILD-TYPE	13	23	70	54	75	31	6	33

Figure S236. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S237. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
20P GAIN MUTATED	42	45	66	38	17
20P GAIN WILD-TYPE	59	107	48	50	41

Figure S237. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S238. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
20P GAIN MUTATED	60	137	58	128	20
20P GAIN WILD-TYPE	339	103	41	136	22

Figure S238. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S239. Gene #36: '20p gain' 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
20P GAIN MUTATED	77	36	77	83	106	13	9
20P GAIN WILD-TYPE	113	107	157	78	138	39	7

Figure S239. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S240. Gene #36: '20p gain' 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
20P GAIN MUTATED	74	69	49	99	87	23
20P GAIN WILD-TYPE	104	174	148	81	97	35

Figure S240. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.13

Table S241. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
20P GAIN MUTATED	91	173	133
20P GAIN WILD-TYPE	215	249	164

Figure S241. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S242. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
20P GAIN MUTATED	41	57	182	54	63
20P GAIN WILD-TYPE	133	129	223	80	63

Figure S242. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S243. Gene #36: '20p gain' 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
20P GAIN MUTATED	52	19	96	45	28	35
20P GAIN WILD-TYPE	75	48	97	90	97	32

Figure S243. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.087

Table S244. Gene #37: '20q gain' 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
20Q GAIN MUTATED	7	13	61	40	35	42	14	10
20Q GAIN WILD-TYPE	14	23	58	56	74	30	6	30

Figure S244. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S245. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
20Q GAIN MUTATED	52	49	70	34	17
20Q GAIN WILD-TYPE	49	103	44	54	41

Figure S245. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S246. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
20Q GAIN MUTATED	64	159	58	136	21
20Q GAIN WILD-TYPE	335	81	41	128	21

Figure S246. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S247. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
20Q GAIN MUTATED	62	71	98	25	39
20Q GAIN WILD-TYPE	70	126	79	63	89

Figure S247. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S248. Gene #37: '20q gain' 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
20Q GAIN MUTATED	82	37	76	82	133	16	10
20Q GAIN WILD-TYPE	108	106	158	79	111	36	6

Figure S248. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S249. Gene #37: '20q gain' 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
20Q GAIN MUTATED	76	72	50	106	106	26
20Q GAIN WILD-TYPE	102	171	147	74	78	32

Figure S249. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S250. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
20Q GAIN MUTATED	95	195	143
20Q GAIN WILD-TYPE	211	227	154

Figure S250. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S251. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
20Q GAIN MUTATED	44	64	206	58	61
20Q GAIN WILD-TYPE	130	122	199	76	65

Figure S251. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S252. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
20Q GAIN MUTATED	122	79	104
20Q GAIN WILD-TYPE	127	177	105

Figure S252. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S253. Gene #37: '20q gain' 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
20Q GAIN MUTATED	58	20	111	52	31	33
20Q GAIN WILD-TYPE	69	47	82	83	94	34

Figure S253. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S254. Gene #38: '21q gain' 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
21Q GAIN MUTATED	2	2	16	31	11	31	8	3
21Q GAIN WILD-TYPE	19	34	103	65	98	41	12	37

Figure S254. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S255. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
21Q GAIN MUTATED	12	15	44	27	6
21Q GAIN WILD-TYPE	89	137	70	61	52

Figure S255. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S256. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
21Q GAIN MUTATED	31	36	22	90	11
21Q GAIN WILD-TYPE	368	204	77	174	31

Figure S256. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S257. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
21Q GAIN MUTATED	47	16	33	10	15
21Q GAIN WILD-TYPE	85	181	144	78	113

Figure S257. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.15

Table S258. Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
21Q GAIN MUTATED	47	16	22
21Q GAIN WILD-TYPE	102	116	95

Figure S258. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S259. Gene #38: '21q gain' 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
21Q GAIN MUTATED	63	10	25	53	32	4	3
21Q GAIN WILD-TYPE	127	133	209	108	212	48	13

Figure S259. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S260. Gene #38: '21q gain' 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
21Q GAIN MUTATED	59	18	15	43	30	25
21Q GAIN WILD-TYPE	119	225	182	137	154	33

Figure S260. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S261. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
21Q GAIN MUTATED	35	62	88
21Q GAIN WILD-TYPE	271	360	209

Figure S261. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S262. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
21Q GAIN MUTATED	12	18	65	44	46
21Q GAIN WILD-TYPE	162	168	340	90	80

Figure S262. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S263. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
21Q GAIN MUTATED	34	27	68
21Q GAIN WILD-TYPE	215	229	141

Figure S263. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S264. Gene #38: '21q gain' 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
21Q GAIN MUTATED	44	5	26	22	7	25
21Q GAIN WILD-TYPE	83	62	167	113	118	42

Figure S264. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S265. Gene #39: '22q gain' 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
22Q GAIN MUTATED	3	0	12	18	2	15	2	0
22Q GAIN WILD-TYPE	18	36	107	78	107	57	18	40

Figure S265. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S266. Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
22Q GAIN MUTATED	9	3	24	15	1
22Q GAIN WILD-TYPE	92	149	90	73	57

Figure S266. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S267. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
22Q GAIN MUTATED	12	22	2	54	5
22Q GAIN WILD-TYPE	387	218	97	210	37

Figure S267. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.18

Table S268. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
22Q GAIN MUTATED	22	8	19	3	9
22Q GAIN WILD-TYPE	110	189	158	85	119

Figure S268. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S269. Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
22Q GAIN MUTATED	31	5	8
22Q GAIN WILD-TYPE	118	127	109

Figure S269. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S270. Gene #39: '22q gain' 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
22Q GAIN MUTATED	34	2	4	30	22	0	2
22Q GAIN WILD-TYPE	156	141	230	131	222	52	14

Figure S270. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S271. Gene #39: '22q gain' 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
22Q GAIN MUTATED	31	2	4	26	18	13
22Q GAIN WILD-TYPE	147	241	193	154	166	45

Figure S271. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S272. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
22Q GAIN MUTATED	7	34	51
22Q GAIN WILD-TYPE	299	388	246

Figure S272. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S273. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
22Q GAIN MUTATED	3	9	34	20	26
22Q GAIN WILD-TYPE	171	177	371	114	100

Figure S273. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S274. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
22Q GAIN MUTATED	18	8	37
22Q GAIN WILD-TYPE	231	248	172

Figure S274. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S275. Gene #39: '22q gain' 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
22Q GAIN MUTATED	22	0	15	10	1	15
22Q GAIN WILD-TYPE	105	67	178	125	124	52

Figure S275. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.24

Table S276. Gene #40: 'xq gain' 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
XQ GAIN MUTATED	2	1	17	25	13	18	4	1
XQ GAIN WILD-TYPE	19	35	102	71	96	54	16	39

Figure S276. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S277. Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
XQ GAIN MUTATED	17	37	17	55	8
XQ GAIN WILD-TYPE	382	203	82	209	34

Figure S277. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.028

Table S278. Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
XQ GAIN MUTATED	26	19	22	4	4
XQ GAIN WILD-TYPE	106	178	155	84	124

Figure S278. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S279. Gene #40: 'xq gain' 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
XQ GAIN MUTATED	43	6	22	23	32	3	4
XQ GAIN WILD-TYPE	147	137	212	138	212	49	12

Figure S279. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S280. Gene #40: 'xq gain' 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
XQ GAIN MUTATED	41	10	18	28	28	8
XQ GAIN WILD-TYPE	137	233	179	152	156	50

Figure S280. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S281. Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
XQ GAIN MUTATED	14	55	58
XQ GAIN WILD-TYPE	292	367	239

Figure S281. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.06

Table S282. Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
XQ GAIN MUTATED	9	19	49	30	20
XQ GAIN WILD-TYPE	165	167	356	104	106

Figure S282. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.048

Table S283. Gene #40: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
XQ GAIN MUTATED	28	14	37
XQ GAIN WILD-TYPE	221	242	172

Figure S283. Get High-res Image Gene #40: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00061 (Fisher's exact test), Q value = 0.22

Table S284. Gene #41: '1p loss' 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
1P LOSS MUTATED	3	7	33	10	28	29	3	7
1P LOSS WILD-TYPE	18	29	86	86	81	43	17	33

Figure S284. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S285. Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
1P LOSS MUTATED	34	23	41	9	13
1P LOSS WILD-TYPE	67	129	73	79	45

Figure S285. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S286. Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
1P LOSS MUTATED	37	95	49	45	11
1P LOSS WILD-TYPE	362	145	50	219	31

Figure S286. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S287. Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
1P LOSS MUTATED	20	40	65	12	17
1P LOSS WILD-TYPE	112	157	112	76	111

Figure S287. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S288. Gene #41: '1p loss' 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
1P LOSS MUTATED	21	12	59	58	73	8	4
1P LOSS WILD-TYPE	169	131	175	103	171	44	12

Figure S288. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S289. Gene #41: '1p loss' 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
1P LOSS MUTATED	21	40	34	70	61	9
1P LOSS WILD-TYPE	157	203	163	110	123	49

Figure S289. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S290. Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
1P LOSS MUTATED	22	34	135	15	25
1P LOSS WILD-TYPE	152	152	270	119	101

Figure S290. Get High-res Image Gene #41: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.048

Table S291. Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
1Q LOSS MUTATED	6	21	4	17	4
1Q LOSS WILD-TYPE	393	219	95	247	38

Figure S291. Get High-res Image Gene #42: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S292. Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
2P LOSS MUTATED	28	76	29	34	10
2P LOSS WILD-TYPE	371	164	70	230	32

Figure S292. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.18

Table S293. Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
2P LOSS MUTATED	14	43	37	9	10
2P LOSS WILD-TYPE	118	154	140	79	118

Figure S293. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.18

Table S294. Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
2P LOSS MUTATED	25	36	10
2P LOSS WILD-TYPE	124	96	107

Figure S294. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.11

Table S295. Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2P LOSS MUTATED	18	10	8	29	6
2P LOSS WILD-TYPE	46	96	82	78	25

Figure S295. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S296. Gene #43: '2p loss' 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
2P LOSS MUTATED	18	15	50	25	64	3	0
2P LOSS WILD-TYPE	172	128	184	136	180	49	16

Figure S296. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S297. Gene #43: '2p loss' 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
2P LOSS MUTATED	16	29	31	43	54	2
2P LOSS WILD-TYPE	162	214	166	137	130	56

Figure S297. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S298. Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
2P LOSS MUTATED	37	100	36
2P LOSS WILD-TYPE	269	322	261

Figure S298. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.037

Table S299. Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
2P LOSS MUTATED	16	39	90	13	15
2P LOSS WILD-TYPE	158	147	315	121	111

Figure S299. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.1

Table S300. Gene #43: '2p loss' 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
2P LOSS MUTATED	12	12	42	31	9	7
2P LOSS WILD-TYPE	115	55	151	104	116	60

Figure S300. Get High-res Image Gene #43: '2p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S301. Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
2Q LOSS MUTATED	29	80	31	49	12
2Q LOSS WILD-TYPE	370	160	68	215	30

Figure S301. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S302. Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
2Q LOSS MUTATED	34	36	9
2Q LOSS WILD-TYPE	115	96	108

Figure S302. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.13

Table S303. Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
2Q LOSS MUTATED	18	8	15	31	7
2Q LOSS WILD-TYPE	46	98	75	76	24

Figure S303. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S304. Gene #44: '2q loss' 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
2Q LOSS MUTATED	31	31	30	48	55	4
2Q LOSS WILD-TYPE	147	212	167	132	129	54

Figure S304. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S305. Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
2Q LOSS MUTATED	39	104	54
2Q LOSS WILD-TYPE	267	318	243

Figure S305. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.22

Table S306. Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
2Q LOSS MUTATED	17	40	95	28	17
2Q LOSS WILD-TYPE	157	146	310	106	109

Figure S306. Get High-res Image Gene #44: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S307. Gene #45: '3p loss' 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
3P LOSS MUTATED	0	7	19	29	4	18	6	4
3P LOSS WILD-TYPE	21	29	100	67	105	54	14	36

Figure S307. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S308. Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
3P LOSS MUTATED	15	18	28	26	0
3P LOSS WILD-TYPE	86	134	86	62	58

Figure S308. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S309. Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
3P LOSS MUTATED	27	49	13	88	4
3P LOSS WILD-TYPE	372	191	86	176	38

Figure S309. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S310. Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
3P LOSS MUTATED	38	15	45	9	17
3P LOSS WILD-TYPE	94	182	132	79	111

Figure S310. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S311. Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
3P LOSS MUTATED	2	14	32	19	7
3P LOSS WILD-TYPE	62	92	58	88	24

Figure S311. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S312. Gene #45: '3p loss' 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
3P LOSS MUTATED	55	14	17	46	39	5	4
3P LOSS WILD-TYPE	135	129	217	115	205	47	12

Figure S312. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S313. Gene #45: '3p loss' 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
3P LOSS MUTATED	54	24	12	48	26	16
3P LOSS WILD-TYPE	124	219	185	132	158	42

Figure S313. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S314. Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
3P LOSS MUTATED	32	53	90
3P LOSS WILD-TYPE	274	369	207

Figure S314. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S315. Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
3P LOSS MUTATED	15	18	72	40	30
3P LOSS WILD-TYPE	159	168	333	94	96

Figure S315. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S316. Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
3P LOSS MUTATED	32	30	62
3P LOSS WILD-TYPE	217	226	147

Figure S316. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S317. Gene #45: '3p loss' 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
3P LOSS MUTATED	37	6	36	16	10	19
3P LOSS WILD-TYPE	90	61	157	119	115	48

Figure S317. Get High-res Image Gene #45: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.064

Table S318. Gene #46: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
3Q LOSS MUTATED	10	7	20	12	0
3Q LOSS WILD-TYPE	91	145	94	76	58

Figure S318. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S319. Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
3Q LOSS MUTATED	12	31	8	45	3
3Q LOSS WILD-TYPE	387	209	91	219	39

Figure S319. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S320. Gene #46: '3q loss' 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
3Q LOSS MUTATED	24	7	9	28	25	4	2
3Q LOSS WILD-TYPE	166	136	225	133	219	48	14

Figure S320. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S321. Gene #46: '3q loss' 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
3Q LOSS MUTATED	23	12	9	30	15	10
3Q LOSS WILD-TYPE	155	231	188	150	169	48

Figure S321. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.072

Table S322. Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
3Q LOSS MUTATED	18	31	46
3Q LOSS WILD-TYPE	288	391	251

Figure S322. Get High-res Image Gene #46: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S323. Gene #47: '4p loss' 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
4P LOSS MUTATED	4	7	25	60	22	41	8	7
4P LOSS WILD-TYPE	17	29	94	36	87	31	12	33

Figure S323. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S324. Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
4P LOSS MUTATED	24	28	57	54	11
4P LOSS WILD-TYPE	77	124	57	34	47

Figure S324. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S325. Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
4P LOSS MUTATED	50	69	46	164	11
4P LOSS WILD-TYPE	349	171	53	100	31

Figure S325. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S326. Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
4P LOSS MUTATED	90	38	53	14	28
4P LOSS WILD-TYPE	42	159	124	74	100

Figure S326. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S327. Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
4P LOSS MUTATED	77	39	25
4P LOSS WILD-TYPE	72	93	92

Figure S327. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S328. Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
4P LOSS MUTATED	18	28	53	29	13
4P LOSS WILD-TYPE	46	78	37	78	18

Figure S328. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S329. Gene #47: '4p loss' 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
4P LOSS MUTATED	122	16	56	78	53	7	6
4P LOSS WILD-TYPE	68	127	178	83	191	45	10

Figure S329. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S330. Gene #47: '4p loss' 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
4P LOSS MUTATED	117	38	37	74	39	33
4P LOSS WILD-TYPE	61	205	160	106	145	25

Figure S330. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S331. Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
4P LOSS MUTATED	48	117	164
4P LOSS WILD-TYPE	258	305	133

Figure S331. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S332. Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
4P LOSS MUTATED	23	39	120	89	58
4P LOSS WILD-TYPE	151	147	285	45	68

Figure S332. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S333. Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
4P LOSS MUTATED	67	43	119
4P LOSS WILD-TYPE	182	213	90

Figure S333. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S334. Gene #47: '4p loss' 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
4P LOSS MUTATED	83	14	64	19	19	30
4P LOSS WILD-TYPE	44	53	129	116	106	37

Figure S334. Get High-res Image Gene #47: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S335. Gene #48: '4q loss' 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
4Q LOSS MUTATED	4	7	24	47	21	36	7	7
4Q LOSS WILD-TYPE	17	29	95	49	88	36	13	33

Figure S335. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S336. Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
4Q LOSS MUTATED	24	26	50	42	11
4Q LOSS WILD-TYPE	77	126	64	46	47

Figure S336. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S337. Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
4Q LOSS MUTATED	47	62	46	138	9
4Q LOSS WILD-TYPE	352	178	53	126	33

Figure S337. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S338. Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
4Q LOSS MUTATED	73	40	46	14	28
4Q LOSS WILD-TYPE	59	157	131	74	100

Figure S338. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S339. Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
4Q LOSS MUTATED	65	35	25
4Q LOSS WILD-TYPE	84	97	92

Figure S339. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S340. Gene #48: '4q loss' 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
4Q LOSS MUTATED	97	15	56	72	49	5	6
4Q LOSS WILD-TYPE	93	128	178	89	195	47	10

Figure S340. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S341. Gene #48: '4q loss' 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
4Q LOSS MUTATED	93	35	37	73	34	28
4Q LOSS WILD-TYPE	85	208	160	107	150	30

Figure S341. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S342. Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
4Q LOSS MUTATED	47	111	133
4Q LOSS WILD-TYPE	259	311	164

Figure S342. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S343. Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
4Q LOSS MUTATED	21	38	112	70	50
4Q LOSS WILD-TYPE	153	148	293	64	76

Figure S343. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S344. Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
4Q LOSS MUTATED	61	40	97
4Q LOSS WILD-TYPE	188	216	112

Figure S344. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S345. Gene #48: '4q loss' 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
4Q LOSS MUTATED	63	13	60	18	17	27
4Q LOSS WILD-TYPE	64	54	133	117	108	40

Figure S345. Get High-res Image Gene #48: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S346. Gene #49: '5p loss' 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
5P LOSS MUTATED	1	1	8	41	5	11	1	2
5P LOSS WILD-TYPE	20	35	111	55	104	61	19	38

Figure S346. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S347. Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
5P LOSS MUTATED	9	5	17	38	1
5P LOSS WILD-TYPE	92	147	97	50	57

Figure S347. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S348. Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
5P LOSS MUTATED	12	16	4	97	6
5P LOSS WILD-TYPE	387	224	95	167	36

Figure S348. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S349. Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
5P LOSS MUTATED	50	8	13	5	16
5P LOSS WILD-TYPE	82	189	164	83	112

Figure S349. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S350. Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
5P LOSS MUTATED	43	9	9
5P LOSS WILD-TYPE	106	123	108

Figure S350. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S351. Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
5P LOSS MUTATED	1	7	38	12	3
5P LOSS WILD-TYPE	63	99	52	95	28

Figure S351. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S352. Gene #49: '5p loss' 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
5P LOSS MUTATED	80	3	7	22	18	3	2
5P LOSS WILD-TYPE	110	140	227	139	226	49	14

Figure S352. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S353. Gene #49: '5p loss' 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
5P LOSS MUTATED	76	8	3	29	12	7
5P LOSS WILD-TYPE	102	235	194	151	172	51

Figure S353. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S354. Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
5P LOSS MUTATED	14	27	91
5P LOSS WILD-TYPE	292	395	206

Figure S354. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S355. Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
5P LOSS MUTATED	3	7	36	60	26
5P LOSS WILD-TYPE	171	179	369	74	100

Figure S355. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S356. Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
5P LOSS MUTATED	12	9	69
5P LOSS WILD-TYPE	237	247	140

Figure S356. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S357. Gene #49: '5p loss' 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
5P LOSS MUTATED	53	3	14	9	0	11
5P LOSS WILD-TYPE	74	64	179	126	125	56

Figure S357. Get High-res Image Gene #49: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S358. Gene #50: '5q loss' 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
5Q LOSS MUTATED	2	4	14	61	4	21	5	3
5Q LOSS WILD-TYPE	19	32	105	35	105	51	15	37

Figure S358. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S359. Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
5Q LOSS MUTATED	14	11	32	56	1
5Q LOSS WILD-TYPE	87	141	82	32	57

Figure S359. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S360. Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
5Q LOSS MUTATED	18	25	5	165	9
5Q LOSS WILD-TYPE	381	215	94	99	33

Figure S360. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S361. Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
5Q LOSS MUTATED	86	8	21	7	30
5Q LOSS WILD-TYPE	46	189	156	81	98

Figure S361. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S362. Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
5Q LOSS MUTATED	69	10	18
5Q LOSS WILD-TYPE	80	122	99

Figure S362. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S363. Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
5Q LOSS MUTATED	3	14	55	19	6
5Q LOSS WILD-TYPE	61	92	35	88	25

Figure S363. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S364. Gene #50: '5q loss' 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
5Q LOSS MUTATED	122	7	8	43	33	4	5
5Q LOSS WILD-TYPE	68	136	226	118	211	48	11

Figure S364. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S365. Gene #50: '5q loss' 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
5Q LOSS MUTATED	117	16	3	46	21	19
5Q LOSS WILD-TYPE	61	227	194	134	163	39

Figure S365. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S366. Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
5Q LOSS MUTATED	19	40	158
5Q LOSS WILD-TYPE	287	382	139

Figure S366. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S367. Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
5Q LOSS MUTATED	4	10	58	94	51
5Q LOSS WILD-TYPE	170	176	347	40	75

Figure S367. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S368. Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
5Q LOSS MUTATED	20	16	114
5Q LOSS WILD-TYPE	229	240	95

Figure S368. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S369. Gene #50: '5q loss' 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
5Q LOSS MUTATED	83	3	25	14	2	23
5Q LOSS WILD-TYPE	44	64	168	121	123	44

Figure S369. Get High-res Image Gene #50: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S370. Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
6P LOSS MUTATED	44	77	19	30	11
6P LOSS WILD-TYPE	355	163	80	234	31

Figure S370. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00064 (Fisher's exact test), Q value = 0.23

Table S371. Gene #51: '6p loss' 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
6P LOSS MUTATED	14	8	53	26	14	9
6P LOSS WILD-TYPE	113	59	140	109	111	58

Figure S371. Get High-res Image Gene #51: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.23

Table S372. Gene #52: '6q loss' 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
6Q LOSS MUTATED	6	13	44	13	23	14	2	14
6Q LOSS WILD-TYPE	15	23	75	83	86	58	18	26

Figure S372. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S373. Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
6Q LOSS MUTATED	73	109	26	38	17
6Q LOSS WILD-TYPE	326	131	73	226	25

Figure S373. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S374. Gene #52: '6q loss' 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
6Q LOSS MUTATED	26	38	58	39	90	10	2
6Q LOSS WILD-TYPE	164	105	176	122	154	42	14

Figure S374. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S375. Gene #52: '6q loss' 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
6Q LOSS MUTATED	24	70	42	44	68	15
6Q LOSS WILD-TYPE	154	173	155	136	116	43

Figure S375. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.087

Table S376. Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
6Q LOSS MUTATED	41	61	117	18	24
6Q LOSS WILD-TYPE	133	125	288	116	102

Figure S376. Get High-res Image Gene #52: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S377. Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
7P LOSS MUTATED	9	39	6	51	2
7P LOSS WILD-TYPE	390	201	93	213	40

Figure S377. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.14

Table S378. Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
7P LOSS MUTATED	25	10	20	6	7
7P LOSS WILD-TYPE	107	187	157	82	121

Figure S378. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S379. Gene #53: '7p loss' 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
7P LOSS MUTATED	31	5	13	21	32	2	2
7P LOSS WILD-TYPE	159	138	221	140	212	50	14

Figure S379. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.037

Table S380. Gene #53: '7p loss' 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
7P LOSS MUTATED	28	11	10	26	26	5
7P LOSS WILD-TYPE	150	232	187	154	158	53

Figure S380. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S381. Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
7P LOSS MUTATED	8	42	55
7P LOSS WILD-TYPE	298	380	242

Figure S381. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.087

Table S382. Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
7P LOSS MUTATED	6	13	45	23	18
7P LOSS WILD-TYPE	168	173	360	111	108

Figure S382. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S383. Gene #53: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
7P LOSS MUTATED	16	12	35
7P LOSS WILD-TYPE	233	244	174

Figure S383. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.22

Table S384. Gene #53: '7p loss' 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
7P LOSS MUTATED	23	2	20	9	4	5
7P LOSS WILD-TYPE	104	65	173	126	121	62

Figure S384. Get High-res Image Gene #53: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S385. Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
7Q LOSS MUTATED	22	43	9	40	2
7Q LOSS WILD-TYPE	377	197	90	224	40

Figure S385. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S386. Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
7Q LOSS MUTATED	13	57	44
7Q LOSS WILD-TYPE	293	365	253

Figure S386. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.2

Table S387. Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
7Q LOSS MUTATED	7	17	59	11	20
7Q LOSS WILD-TYPE	167	169	346	123	106

Figure S387. Get High-res Image Gene #54: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S388. Gene #55: '8p loss' 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
8P LOSS MUTATED	4	10	56	45	20	37	11	17
8P LOSS WILD-TYPE	17	26	63	51	89	35	9	23

Figure S388. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.028

Table S389. Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
8P LOSS MUTATED	48	44	57	39	12
8P LOSS WILD-TYPE	53	108	57	49	46

Figure S389. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S390. Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
8P LOSS MUTATED	91	117	18	138	18
8P LOSS WILD-TYPE	308	123	81	126	24

Figure S390. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S391. Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
8P LOSS MUTATED	57	52	78	16	49
8P LOSS WILD-TYPE	75	145	99	72	79

Figure S391. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.024

Table S392. Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
8P LOSS MUTATED	9	49	40	50	15
8P LOSS WILD-TYPE	55	57	50	57	16

Figure S392. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S393. Gene #55: '8p loss' 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
8P LOSS MUTATED	81	35	48	83	104	18	10
8P LOSS WILD-TYPE	109	108	186	78	140	34	6

Figure S393. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S394. Gene #55: '8p loss' 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
8P LOSS MUTATED	73	71	35	88	78	34
8P LOSS WILD-TYPE	105	172	162	92	106	24

Figure S394. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S395. Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
8P LOSS MUTATED	81	157	138
8P LOSS WILD-TYPE	225	265	159

Figure S395. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S396. Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
8P LOSS MUTATED	42	54	157	60	63
8P LOSS WILD-TYPE	132	132	248	74	63

Figure S396. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.06

Table S397. Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
8P LOSS MUTATED	94	68	94
8P LOSS WILD-TYPE	155	188	115

Figure S397. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.1

Table S398. Gene #55: '8p loss' 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
8P LOSS MUTATED	55	15	82	42	31	31
8P LOSS WILD-TYPE	72	52	111	93	94	36

Figure S398. Get High-res Image Gene #55: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S399. Gene #57: '9p loss' 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
9P LOSS MUTATED	7	10	53	30	18	33	9	6
9P LOSS WILD-TYPE	14	26	66	66	91	39	11	34

Figure S399. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S400. Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
9P LOSS MUTATED	43	30	59	25	9
9P LOSS WILD-TYPE	58	122	55	63	49

Figure S400. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S401. Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
9P LOSS MUTATED	36	141	18	105	10
9P LOSS WILD-TYPE	363	99	81	159	32

Figure S401. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S402. Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
9P LOSS MUTATED	49	42	76	13	25
9P LOSS WILD-TYPE	83	155	101	75	103

Figure S402. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S403. Gene #57: '9p loss' 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
9P LOSS MUTATED	56	19	40	69	107	10	8
9P LOSS WILD-TYPE	134	124	194	92	137	42	8

Figure S403. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S404. Gene #57: '9p loss' 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
9P LOSS MUTATED	50	35	28	83	86	27
9P LOSS WILD-TYPE	128	208	169	97	98	31

Figure S404. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S405. Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
9P LOSS MUTATED	47	147	109
9P LOSS WILD-TYPE	259	275	188

Figure S405. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S406. Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
9P LOSS MUTATED	16	44	148	37	58
9P LOSS WILD-TYPE	158	142	257	97	68

Figure S406. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S407. Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
9P LOSS MUTATED	73	45	83
9P LOSS WILD-TYPE	176	211	126

Figure S407. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S408. Gene #57: '9p loss' 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
9P LOSS MUTATED	39	7	66	42	12	35
9P LOSS WILD-TYPE	88	60	127	93	113	32

Figure S408. Get High-res Image Gene #57: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S409. Gene #58: '9q loss' 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
9Q LOSS MUTATED	7	5	42	40	19	23	7	5
9Q LOSS WILD-TYPE	14	31	77	56	90	49	13	35

Figure S409. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S410. Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
9Q LOSS MUTATED	36	23	47	34	8
9Q LOSS WILD-TYPE	65	129	67	54	50

Figure S410. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S411. Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
9Q LOSS MUTATED	31	111	17	107	12
9Q LOSS WILD-TYPE	368	129	82	157	30

Figure S411. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S412. Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
9Q LOSS MUTATED	57	40	57	10	22
9Q LOSS WILD-TYPE	75	157	120	78	106

Figure S412. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S413. Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
9Q LOSS MUTATED	65	29	22
9Q LOSS WILD-TYPE	84	103	95

Figure S413. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S414. Gene #58: '9q loss' 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
9Q LOSS MUTATED	73	13	40	46	91	7	7
9Q LOSS WILD-TYPE	117	130	194	115	153	45	9

Figure S414. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S415. Gene #58: '9q loss' 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
9Q LOSS MUTATED	66	27	25	68	71	20
9Q LOSS WILD-TYPE	112	216	172	112	113	38

Figure S415. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S416. Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
9Q LOSS MUTATED	38	116	115
9Q LOSS WILD-TYPE	268	306	182

Figure S416. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S417. Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
9Q LOSS MUTATED	13	33	119	53	51
9Q LOSS WILD-TYPE	161	153	286	81	75

Figure S417. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S418. Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
9Q LOSS MUTATED	55	39	84
9Q LOSS WILD-TYPE	194	217	125

Figure S418. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S419. Gene #58: '9q loss' 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
9Q LOSS MUTATED	48	5	52	32	10	31
9Q LOSS WILD-TYPE	79	62	141	103	115	36

Figure S419. Get High-res Image Gene #58: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S420. Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
10P LOSS MUTATED	31	53	21	54	9
10P LOSS WILD-TYPE	368	187	78	210	33

Figure S420. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.093

Table S421. Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
10P LOSS MUTATED	35	31	35	12	8
10P LOSS WILD-TYPE	97	166	142	76	120

Figure S421. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.09

Table S422. Gene #59: '10p loss' 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
10P LOSS MUTATED	37	11	30	38	47	4	0
10P LOSS WILD-TYPE	153	132	204	123	197	48	16

Figure S422. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.056

Table S423. Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
10P LOSS MUTATED	10	28	73	24	30
10P LOSS WILD-TYPE	164	158	332	110	96

Figure S423. Get High-res Image Gene #59: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S424. Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
10Q LOSS MUTATED	34	65	21	92	13
10Q LOSS WILD-TYPE	365	175	78	172	29

Figure S424. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S425. Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
10Q LOSS MUTATED	55	34	53	11	12
10Q LOSS WILD-TYPE	77	163	124	77	116

Figure S425. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S426. Gene #60: '10q loss' 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
10Q LOSS MUTATED	66	13	32	49	61	3	0
10Q LOSS WILD-TYPE	124	130	202	112	183	49	16

Figure S426. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S427. Gene #60: '10q loss' 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
10Q LOSS MUTATED	59	24	24	57	45	15
10Q LOSS WILD-TYPE	119	219	173	123	139	43

Figure S427. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S428. Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
10Q LOSS MUTATED	45	82	93
10Q LOSS WILD-TYPE	261	340	204

Figure S428. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S429. Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
10Q LOSS MUTATED	13	28	94	41	44
10Q LOSS WILD-TYPE	161	158	311	93	82

Figure S429. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.028

Table S430. Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
10Q LOSS MUTATED	51	39	68
10Q LOSS WILD-TYPE	198	217	141

Figure S430. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S431. Gene #60: '10q loss' 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
10Q LOSS MUTATED	47	7	46	30	11	17
10Q LOSS WILD-TYPE	80	60	147	105	114	50

Figure S431. Get High-res Image Gene #60: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S432. Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
11P LOSS MUTATED	39	94	26	101	7
11P LOSS WILD-TYPE	360	146	73	163	35

Figure S432. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S433. Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
11P LOSS MUTATED	46	35	63	13	21
11P LOSS WILD-TYPE	86	162	114	75	107

Figure S433. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.24

Table S434. Gene #61: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
11P LOSS MUTATED	9	22	33	34	15
11P LOSS WILD-TYPE	55	84	57	73	16

Figure S434. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S435. Gene #61: '11p loss' 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
11P LOSS MUTATED	58	20	31	57	85	12	4
11P LOSS WILD-TYPE	132	123	203	104	159	40	12

Figure S435. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S436. Gene #61: '11p loss' 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
11P LOSS MUTATED	54	37	24	69	63	20
11P LOSS WILD-TYPE	124	206	173	111	121	38

Figure S436. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S437. Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
11P LOSS MUTATED	56	100	103
11P LOSS WILD-TYPE	250	322	194

Figure S437. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S438. Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
11P LOSS MUTATED	20	38	116	40	45
11P LOSS WILD-TYPE	154	148	289	94	81

Figure S438. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.052

Table S439. Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
11P LOSS MUTATED	58	44	73
11P LOSS WILD-TYPE	191	212	136

Figure S439. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.068

Table S440. Gene #61: '11p loss' 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
11P LOSS MUTATED	42	9	58	30	16	20
11P LOSS WILD-TYPE	85	58	135	105	109	47

Figure S440. Get High-res Image Gene #61: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.06

Table S441. Gene #62: '11q loss' 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
11Q LOSS MUTATED	5	16	64	27	26	26	6	15
11Q LOSS WILD-TYPE	16	20	55	69	83	46	14	25

Figure S441. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S442. Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
11Q LOSS MUTATED	57	49	42	24	13
11Q LOSS WILD-TYPE	44	103	72	64	45

Figure S442. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S443. Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
11Q LOSS MUTATED	75	141	34	94	10
11Q LOSS WILD-TYPE	324	99	65	170	32

Figure S443. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.048

Table S444. Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
11Q LOSS MUTATED	44	67	81	21	28
11Q LOSS WILD-TYPE	88	130	96	67	100

Figure S444. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S445. Gene #62: '11q loss' 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
11Q LOSS MUTATED	54	41	50	54	133	17	4
11Q LOSS WILD-TYPE	136	102	184	107	111	35	12

Figure S445. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S446. Gene #62: '11q loss' 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
11Q LOSS MUTATED	51	75	31	75	103	18
11Q LOSS WILD-TYPE	127	168	166	105	81	40

Figure S446. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00046 (Fisher's exact test), Q value = 0.18

Table S447. Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
11Q LOSS MUTATED	38	62	162	39	45
11Q LOSS WILD-TYPE	136	124	243	95	81

Figure S447. Get High-res Image Gene #62: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S448. Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
12P LOSS MUTATED	33	33	11	66	2
12P LOSS WILD-TYPE	366	207	88	198	40

Figure S448. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S449. Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
12P LOSS MUTATED	40	16	21	11	11
12P LOSS WILD-TYPE	92	181	156	77	117

Figure S449. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S450. Gene #63: '12p loss' 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
12P LOSS MUTATED	52	13	19	24	30	4	2
12P LOSS WILD-TYPE	138	130	215	137	214	48	14

Figure S450. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S451. Gene #63: '12p loss' 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
12P LOSS MUTATED	47	21	14	25	23	14
12P LOSS WILD-TYPE	131	222	183	155	161	44

Figure S451. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S452. Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
12P LOSS MUTATED	25	46	72
12P LOSS WILD-TYPE	281	376	225

Figure S452. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S453. Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
12P LOSS MUTATED	10	19	51	35	28
12P LOSS WILD-TYPE	164	167	354	99	98

Figure S453. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S454. Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
12P LOSS MUTATED	26	21	52
12P LOSS WILD-TYPE	223	235	157

Figure S454. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S455. Gene #63: '12p loss' 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
12P LOSS MUTATED	34	4	24	15	7	15
12P LOSS WILD-TYPE	93	63	169	120	118	52

Figure S455. Get High-res Image Gene #63: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S456. Gene #64: '12q loss' 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
12Q LOSS MUTATED	2	3	7	33	5	5	2	2
12Q LOSS WILD-TYPE	19	33	112	63	104	67	18	38

Figure S456. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S457. Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
12Q LOSS MUTATED	5	7	15	28	4
12Q LOSS WILD-TYPE	96	145	99	60	54

Figure S457. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S458. Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
12Q LOSS MUTATED	19	18	11	74	3
12Q LOSS WILD-TYPE	380	222	88	190	39

Figure S458. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S459. Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
12Q LOSS MUTATED	50	8	17	6	8
12Q LOSS WILD-TYPE	82	189	160	82	120

Figure S459. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.076

Table S460. Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
12Q LOSS MUTATED	32	9	8
12Q LOSS WILD-TYPE	117	123	109

Figure S460. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S461. Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
12Q LOSS MUTATED	8	5	28	4	4
12Q LOSS WILD-TYPE	56	101	62	103	27

Figure S461. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S462. Gene #64: '12q loss' 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
12Q LOSS MUTATED	65	8	14	15	18	3	1
12Q LOSS WILD-TYPE	125	135	220	146	226	49	15

Figure S462. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S463. Gene #64: '12q loss' 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
12Q LOSS MUTATED	60	14	8	17	13	12
12Q LOSS WILD-TYPE	118	229	189	163	171	46

Figure S463. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S464. Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
12Q LOSS MUTATED	20	24	78
12Q LOSS WILD-TYPE	286	398	219

Figure S464. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S465. Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
12Q LOSS MUTATED	7	10	33	45	27
12Q LOSS WILD-TYPE	167	176	372	89	99

Figure S465. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S466. Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
12Q LOSS MUTATED	17	17	61
12Q LOSS WILD-TYPE	232	239	148

Figure S466. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S467. Gene #64: '12q loss' 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
12Q LOSS MUTATED	44	2	19	11	6	13
12Q LOSS WILD-TYPE	83	65	174	124	119	54

Figure S467. Get High-res Image Gene #64: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.037

Table S468. Gene #65: '13q loss' 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
13Q LOSS MUTATED	7	14	62	51	30	38	9	8
13Q LOSS WILD-TYPE	14	22	57	45	79	34	11	32

Figure S468. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S469. Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
13Q LOSS MUTATED	58	40	62	47	12
13Q LOSS WILD-TYPE	43	112	52	41	46

Figure S469. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S470. Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
13Q LOSS MUTATED	78	131	55	138	24
13Q LOSS WILD-TYPE	321	109	44	126	18

Figure S470. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S471. Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
13Q LOSS MUTATED	77	70	87	18	39
13Q LOSS WILD-TYPE	55	127	90	70	89

Figure S471. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S472. Gene #65: '13q loss' 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
13Q LOSS MUTATED	104	39	73	76	110	13	10
13Q LOSS WILD-TYPE	86	104	161	85	134	39	6

Figure S472. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S473. Gene #65: '13q loss' 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
13Q LOSS MUTATED	97	69	49	92	93	25
13Q LOSS WILD-TYPE	81	174	148	88	91	33

Figure S473. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S474. Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
13Q LOSS MUTATED	85	180	154
13Q LOSS WILD-TYPE	221	242	143

Figure S474. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S475. Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
13Q LOSS MUTATED	39	72	176	75	57
13Q LOSS WILD-TYPE	135	114	229	59	69

Figure S475. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S476. Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
13Q LOSS MUTATED	91	75	113
13Q LOSS WILD-TYPE	158	181	96

Figure S476. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S477. Gene #65: '13q loss' 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
13Q LOSS MUTATED	69	16	85	52	26	31
13Q LOSS WILD-TYPE	58	51	108	83	99	36

Figure S477. Get High-res Image Gene #65: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S478. Gene #66: '14q loss' 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
14Q LOSS MUTATED	3	1	30	50	7	14	9	5
14Q LOSS WILD-TYPE	18	35	89	46	102	58	11	35

Figure S478. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S479. Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
14Q LOSS MUTATED	24	17	29	47	2
14Q LOSS WILD-TYPE	77	135	85	41	56

Figure S479. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S480. Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
14Q LOSS MUTATED	33	54	20	139	9
14Q LOSS WILD-TYPE	366	186	79	125	33

Figure S480. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S481. Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
14Q LOSS MUTATED	79	24	40	11	28
14Q LOSS WILD-TYPE	53	173	137	77	100

Figure S481. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S482. Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
14Q LOSS MUTATED	54	16	25
14Q LOSS WILD-TYPE	95	116	92

Figure S482. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S483. Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
14Q LOSS MUTATED	4	20	44	22	5
14Q LOSS WILD-TYPE	60	86	46	85	26

Figure S483. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S484. Gene #66: '14q loss' 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
14Q LOSS MUTATED	111	15	20	36	61	7	5
14Q LOSS WILD-TYPE	79	128	214	125	183	45	11

Figure S484. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S485. Gene #66: '14q loss' 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
14Q LOSS MUTATED	106	24	16	62	36	11
14Q LOSS WILD-TYPE	72	219	181	118	148	47

Figure S485. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S486. Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
14Q LOSS MUTATED	42	69	137
14Q LOSS WILD-TYPE	264	353	160

Figure S486. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S487. Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
14Q LOSS MUTATED	16	24	77	85	46
14Q LOSS WILD-TYPE	158	162	328	49	80

Figure S487. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S488. Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
14Q LOSS MUTATED	44	38	104
14Q LOSS WILD-TYPE	205	218	105

Figure S488. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S489. Gene #66: '14q loss' 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
14Q LOSS MUTATED	76	9	47	20	14	20
14Q LOSS WILD-TYPE	51	58	146	115	111	47

Figure S489. Get High-res Image Gene #66: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.02

Table S490. Gene #67: '15q loss' 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
15Q LOSS MUTATED	4	9	31	45	22	33	8	6
15Q LOSS WILD-TYPE	17	27	88	51	87	39	12	34

Figure S490. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S491. Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
15Q LOSS MUTATED	27	28	48	43	12
15Q LOSS WILD-TYPE	74	124	66	45	46

Figure S491. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S492. Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
15Q LOSS MUTATED	36	79	45	139	13
15Q LOSS WILD-TYPE	363	161	54	125	29

Figure S492. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S493. Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
15Q LOSS MUTATED	74	39	59	15	28
15Q LOSS WILD-TYPE	58	158	118	73	100

Figure S493. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S494. Gene #67: '15q loss' 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
15Q LOSS MUTATED	96	16	50	66	71	5	6
15Q LOSS WILD-TYPE	94	127	184	95	173	47	10

Figure S494. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S495. Gene #67: '15q loss' 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
15Q LOSS MUTATED	93	37	30	78	56	16
15Q LOSS WILD-TYPE	85	206	167	102	128	42

Figure S495. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S496. Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
15Q LOSS MUTATED	47	117	139
15Q LOSS WILD-TYPE	259	305	158

Figure S496. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S497. Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
15Q LOSS MUTATED	20	32	126	73	52
15Q LOSS WILD-TYPE	154	154	279	61	74

Figure S497. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S498. Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
15Q LOSS MUTATED	72	43	92
15Q LOSS WILD-TYPE	177	213	117

Figure S498. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S499. Gene #67: '15q loss' 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
15Q LOSS MUTATED	63	9	67	26	15	27
15Q LOSS WILD-TYPE	64	58	126	109	110	40

Figure S499. Get High-res Image Gene #67: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S500. Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
16P LOSS MUTATED	47	36	10	65	7
16P LOSS WILD-TYPE	352	204	89	199	35

Figure S500. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.18

Table S501. Gene #68: '16p loss' 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
16P LOSS MUTATED	50	18	28	27	34	3	4
16P LOSS WILD-TYPE	140	125	206	134	210	49	12

Figure S501. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.037

Table S502. Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
16P LOSS MUTATED	38	54	71
16P LOSS WILD-TYPE	268	368	226

Figure S502. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.064

Table S503. Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
16P LOSS MUTATED	29	36	54
16P LOSS WILD-TYPE	220	220	155

Figure S503. Get High-res Image Gene #68: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S504. Gene #69: '16q loss' 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
16Q LOSS MUTATED	12	21	62	26	82	38	13	31
16Q LOSS WILD-TYPE	9	15	57	70	27	34	7	9

Figure S504. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S505. Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
16Q LOSS MUTATED	57	105	59	22	42
16Q LOSS WILD-TYPE	44	47	55	66	16

Figure S505. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S506. Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
16Q LOSS MUTATED	245	126	76	107	26
16Q LOSS WILD-TYPE	154	114	23	157	16

Figure S506. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S507. Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
16Q LOSS MUTATED	51	131	102	57	59
16Q LOSS WILD-TYPE	81	66	75	31	69

Figure S507. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S508. Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
16Q LOSS MUTATED	57	87	67
16Q LOSS WILD-TYPE	92	45	50

Figure S508. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S509. Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
16Q LOSS MUTATED	48	62	26	64	11
16Q LOSS WILD-TYPE	16	44	64	43	20

Figure S509. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S510. Gene #69: '16q loss' 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
16Q LOSS MUTATED	62	93	179	80	119	35	9
16Q LOSS WILD-TYPE	128	50	55	81	125	17	7

Figure S510. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S511. Gene #69: '16q loss' 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
16Q LOSS MUTATED	58	158	142	103	100	16
16Q LOSS WILD-TYPE	120	85	55	77	84	42

Figure S511. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S512. Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
16Q LOSS MUTATED	196	265	110
16Q LOSS WILD-TYPE	110	157	187

Figure S512. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S513. Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
16Q LOSS MUTATED	122	113	241	51	44
16Q LOSS WILD-TYPE	52	73	164	83	82

Figure S513. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S514. Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
16Q LOSS MUTATED	145	166	84
16Q LOSS WILD-TYPE	104	90	125

Figure S514. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S515. Gene #69: '16q loss' 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
16Q LOSS MUTATED	45	42	119	66	95	28
16Q LOSS WILD-TYPE	82	25	74	69	30	39

Figure S515. Get High-res Image Gene #69: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S516. Gene #70: '17p loss' 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
17P LOSS MUTATED	13	23	66	60	30	57	12	21
17P LOSS WILD-TYPE	8	13	53	36	79	15	8	19

Figure S516. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S517. Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
17P LOSS MUTATED	57	76	85	53	11
17P LOSS WILD-TYPE	44	76	29	35	47

Figure S517. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S518. Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
17P LOSS MUTATED	141	155	46	195	21
17P LOSS WILD-TYPE	258	85	53	69	21

Figure S518. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S519. Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
17P LOSS MUTATED	82	90	112	37	52
17P LOSS WILD-TYPE	50	107	65	51	76

Figure S519. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S520. Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
17P LOSS MUTATED	109	55	55
17P LOSS WILD-TYPE	40	77	62

Figure S520. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S521. Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
17P LOSS MUTATED	21	47	60	68	23
17P LOSS WILD-TYPE	43	59	30	39	8

Figure S521. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S522. Gene #70: '17p loss' 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
17P LOSS MUTATED	113	67	75	123	146	21	11
17P LOSS WILD-TYPE	77	76	159	38	98	31	5

Figure S522. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S523. Gene #70: '17p loss' 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
17P LOSS MUTATED	106	118	51	134	105	42
17P LOSS WILD-TYPE	72	125	146	46	79	16

Figure S523. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S524. Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
17P LOSS MUTATED	130	221	197
17P LOSS WILD-TYPE	176	201	100

Figure S524. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S525. Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
17P LOSS MUTATED	62	80	242	88	76
17P LOSS WILD-TYPE	112	106	163	46	50

Figure S525. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.033

Table S526. Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
17P LOSS MUTATED	128	113	135
17P LOSS WILD-TYPE	121	143	74

Figure S526. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S527. Gene #70: '17p loss' 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
17P LOSS MUTATED	75	29	117	63	45	47
17P LOSS WILD-TYPE	52	38	76	72	80	20

Figure S527. Get High-res Image Gene #70: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S528. Gene #71: '17q loss' 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
17Q LOSS MUTATED	3	4	22	48	12	34	4	12
17Q LOSS WILD-TYPE	18	32	97	48	97	38	16	28

Figure S528. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S529. Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
17Q LOSS MUTATED	20	26	46	42	5
17Q LOSS WILD-TYPE	81	126	68	46	53

Figure S529. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S530. Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
17Q LOSS MUTATED	53	51	23	130	6
17Q LOSS WILD-TYPE	346	189	76	134	36

Figure S530. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S531. Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
17Q LOSS MUTATED	65	26	31	11	30
17Q LOSS WILD-TYPE	67	171	146	77	98

Figure S531. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S532. Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	149	132	117
17Q LOSS MUTATED	71	15	29
17Q LOSS WILD-TYPE	78	117	88

Figure S532. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S533. Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
17Q LOSS MUTATED	8	23	49	20	15
17Q LOSS WILD-TYPE	56	83	41	87	16

Figure S533. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S534. Gene #71: '17q loss' 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
17Q LOSS MUTATED	85	18	30	72	44	10	3
17Q LOSS WILD-TYPE	105	125	204	89	200	42	13

Figure S534. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S535. Gene #71: '17q loss' 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
17Q LOSS MUTATED	82	47	14	60	27	32
17Q LOSS WILD-TYPE	96	196	183	120	157	26

Figure S535. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S536. Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
17Q LOSS MUTATED	50	84	124
17Q LOSS WILD-TYPE	256	338	173

Figure S536. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S537. Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
17Q LOSS MUTATED	24	18	99	68	49
17Q LOSS WILD-TYPE	150	168	306	66	77

Figure S537. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S538. Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
17Q LOSS MUTATED	49	45	85
17Q LOSS WILD-TYPE	200	211	124

Figure S538. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S539. Gene #71: '17q loss' 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
17Q LOSS MUTATED	55	9	52	14	18	31
17Q LOSS WILD-TYPE	72	58	141	121	107	36

Figure S539. Get High-res Image Gene #71: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.093

Table S540. Gene #72: '18p loss' 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
18P LOSS MUTATED	6	11	35	27	19	38	9	13
18P LOSS WILD-TYPE	15	25	84	69	90	34	11	27

Figure S540. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.14

Table S541. Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18P LOSS MUTATED	28	39	55	24	12
18P LOSS WILD-TYPE	73	113	59	64	46

Figure S541. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S542. Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
18P LOSS MUTATED	63	103	37	97	10
18P LOSS WILD-TYPE	336	137	62	167	32

Figure S542. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S543. Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18P LOSS MUTATED	37	40	88	16	31
18P LOSS WILD-TYPE	95	157	89	72	97

Figure S543. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S544. Gene #72: '18p loss' 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
18P LOSS MUTATED	50	25	45	85	80	15	9
18P LOSS WILD-TYPE	140	118	189	76	164	37	7

Figure S544. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S545. Gene #72: '18p loss' 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
18P LOSS MUTATED	48	63	30	94	53	21
18P LOSS WILD-TYPE	130	180	167	86	131	37

Figure S545. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S546. Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
18P LOSS MUTATED	30	48	149	33	47
18P LOSS WILD-TYPE	144	138	256	101	79

Figure S546. Get High-res Image Gene #72: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.11

Table S547. Gene #73: '18q loss' 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
18Q LOSS MUTATED	5	11	34	27	19	38	7	9
18Q LOSS WILD-TYPE	16	25	85	69	90	34	13	31

Figure S547. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.087

Table S548. Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
18Q LOSS MUTATED	27	34	53	25	11
18Q LOSS WILD-TYPE	74	118	61	63	47

Figure S548. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S549. Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
18Q LOSS MUTATED	61	101	38	103	9
18Q LOSS WILD-TYPE	338	139	61	161	33

Figure S549. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S550. Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
18Q LOSS MUTATED	46	43	86	15	28
18Q LOSS WILD-TYPE	86	154	91	73	100

Figure S550. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S551. Gene #73: '18q loss' 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
18Q LOSS MUTATED	57	26	46	81	79	13	8
18Q LOSS WILD-TYPE	133	117	188	80	165	39	8

Figure S551. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S552. Gene #73: '18q loss' 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
18Q LOSS MUTATED	55	58	28	96	49	24
18Q LOSS WILD-TYPE	123	185	169	84	135	34

Figure S552. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S553. Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
18Q LOSS MUTATED	31	44	137	40	55
18Q LOSS WILD-TYPE	143	142	268	94	71

Figure S553. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.25

Table S554. Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
18Q LOSS MUTATED	78	56	79
18Q LOSS WILD-TYPE	171	200	130

Figure S554. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.1

Table S555. Gene #73: '18q loss' 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
18Q LOSS MUTATED	43	14	73	28	27	28
18Q LOSS WILD-TYPE	84	53	120	107	98	39

Figure S555. Get High-res Image Gene #73: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S556. Gene #74: '19p loss' 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
19P LOSS MUTATED	3	6	30	20	8	25	1	2
19P LOSS WILD-TYPE	18	30	89	76	101	47	19	38

Figure S556. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S557. Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
19P LOSS MUTATED	29	13	33	18	2
19P LOSS WILD-TYPE	72	139	81	70	56

Figure S557. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S558. Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
19P LOSS MUTATED	17	85	8	70	7
19P LOSS WILD-TYPE	382	155	91	194	35

Figure S558. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S559. Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
19P LOSS MUTATED	35	21	48	5	15
19P LOSS WILD-TYPE	97	176	129	83	113

Figure S559. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.048

Table S560. Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	64	106	90	107	31
19P LOSS MUTATED	3	13	21	27	11
19P LOSS WILD-TYPE	61	93	69	80	20

Figure S560. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S561. Gene #74: '19p loss' 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
19P LOSS MUTATED	45	8	17	45	66	4	2
19P LOSS WILD-TYPE	145	135	217	116	178	48	14

Figure S561. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S562. Gene #74: '19p loss' 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
19P LOSS MUTATED	42	15	10	64	46	10
19P LOSS WILD-TYPE	136	228	187	116	138	48

Figure S562. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S563. Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
19P LOSS MUTATED	19	80	83
19P LOSS WILD-TYPE	287	342	214

Figure S563. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S564. Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
19P LOSS MUTATED	4	26	89	32	31
19P LOSS WILD-TYPE	170	160	316	102	95

Figure S564. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S565. Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
19P LOSS MUTATED	41	21	63
19P LOSS WILD-TYPE	208	235	146

Figure S565. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S566. Gene #74: '19p loss' 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
19P LOSS MUTATED	32	2	42	25	4	20
19P LOSS WILD-TYPE	95	65	151	110	121	47

Figure S566. Get High-res Image Gene #74: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S567. Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
19Q LOSS MUTATED	24	10	30	11	2
19Q LOSS WILD-TYPE	77	142	84	77	56

Figure S567. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S568. Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
19Q LOSS MUTATED	14	76	5	54	7
19Q LOSS WILD-TYPE	385	164	94	210	35

Figure S568. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S569. Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
19Q LOSS MUTATED	27	17	43	2	15
19Q LOSS WILD-TYPE	105	180	134	86	113

Figure S569. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S570. Gene #75: '19q loss' 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
19Q LOSS MUTATED	33	7	15	43	54	3	1
19Q LOSS WILD-TYPE	157	136	219	118	190	49	15

Figure S570. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S571. Gene #75: '19q loss' 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
19Q LOSS MUTATED	33	11	10	49	43	10
19Q LOSS WILD-TYPE	145	232	187	131	141	48

Figure S571. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S572. Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
19Q LOSS MUTATED	16	68	68
19Q LOSS WILD-TYPE	290	354	229

Figure S572. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S573. Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
19Q LOSS MUTATED	3	28	73	28	20
19Q LOSS WILD-TYPE	171	158	332	106	106

Figure S573. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S574. Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
19Q LOSS MUTATED	35	15	51
19Q LOSS WILD-TYPE	214	241	158

Figure S574. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S575. Gene #75: '19q loss' 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
19Q LOSS MUTATED	27	2	29	25	2	16
19Q LOSS WILD-TYPE	100	65	164	110	123	51

Figure S575. Get High-res Image Gene #75: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.045

Table S576. Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	101	152	114	88	58
20P LOSS MUTATED	9	4	12	14	0
20P LOSS WILD-TYPE	92	148	102	74	58

Figure S576. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S577. Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
20P LOSS MUTATED	10	24	5	46	3
20P LOSS WILD-TYPE	389	216	94	218	39

Figure S577. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S578. Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
20P LOSS MUTATED	33	6	17	5	3
20P LOSS WILD-TYPE	99	191	160	83	125

Figure S578. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S579. Gene #76: '20p loss' 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
20P LOSS MUTATED	41	4	8	11	23	0	1
20P LOSS WILD-TYPE	149	139	226	150	221	52	15

Figure S579. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S580. Gene #76: '20p loss' 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
20P LOSS MUTATED	39	3	5	21	15	5
20P LOSS WILD-TYPE	139	240	192	159	169	53

Figure S580. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S581. Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
20P LOSS MUTATED	10	24	48
20P LOSS WILD-TYPE	296	398	249

Figure S581. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S582. Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
20P LOSS MUTATED	5	6	31	31	9
20P LOSS WILD-TYPE	169	180	374	103	117

Figure S582. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S583. Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
20P LOSS MUTATED	10	11	36
20P LOSS WILD-TYPE	239	245	173

Figure S583. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S584. Gene #76: '20p loss' 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
20P LOSS MUTATED	28	0	10	10	4	5
20P LOSS WILD-TYPE	99	67	183	125	121	62

Figure S584. Get High-res Image Gene #76: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S585. Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
20Q LOSS MUTATED	5	11	4	28	2
20Q LOSS WILD-TYPE	394	229	95	236	40

Figure S585. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S586. Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
20Q LOSS MUTATED	23	5	4	3	1
20Q LOSS WILD-TYPE	109	192	173	85	127

Figure S586. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S587. Gene #77: '20q loss' 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
20Q LOSS MUTATED	28	4	4	5	9	0	0
20Q LOSS WILD-TYPE	162	139	230	156	235	52	16

Figure S587. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S588. Gene #77: '20q loss' 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
20Q LOSS MUTATED	27	3	3	8	7	2
20Q LOSS WILD-TYPE	151	240	194	172	177	56

Figure S588. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S589. Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
20Q LOSS MUTATED	8	10	29
20Q LOSS WILD-TYPE	298	412	268

Figure S589. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S590. Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	174	186	405	134	126
20Q LOSS MUTATED	4	2	13	20	8
20Q LOSS WILD-TYPE	170	184	392	114	118

Figure S590. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S591. Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	249	256	209
20Q LOSS MUTATED	2	8	24
20Q LOSS WILD-TYPE	247	248	185

Figure S591. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S592. Gene #77: '20q loss' 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
20Q LOSS MUTATED	20	0	1	7	3	3
20Q LOSS WILD-TYPE	107	67	192	128	122	64

Figure S592. Get High-res Image Gene #77: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S593. Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
21Q LOSS MUTATED	23	69	17	52	10
21Q LOSS WILD-TYPE	376	171	82	212	32

Figure S593. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.18

Table S594. Gene #78: '21q loss' 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
21Q LOSS MUTATED	31	27	20	45	38	9
21Q LOSS WILD-TYPE	147	216	177	135	146	49

Figure S594. Get High-res Image Gene #78: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S595. Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
22Q LOSS MUTATED	127	137	69	116	22
22Q LOSS WILD-TYPE	272	103	30	148	20

Figure S595. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.041

Table S596. Gene #79: '22q loss' 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
22Q LOSS MUTATED	69	114	77	97	98	15
22Q LOSS WILD-TYPE	109	129	120	83	86	43

Figure S596. Get High-res Image Gene #79: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S597. Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	399	240	99	264	42
XQ LOSS MUTATED	26	61	13	71	5
XQ LOSS WILD-TYPE	373	179	86	193	37

Figure S597. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.011

Table S598. Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	132	197	177	88	128
XQ LOSS MUTATED	31	29	45	6	8
XQ LOSS WILD-TYPE	101	168	132	82	120

Figure S598. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.015

Table S599. Gene #80: 'xq loss' 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
XQ LOSS MUTATED	40	13	25	32	61	5	0
XQ LOSS WILD-TYPE	150	130	209	129	183	47	16

Figure S599. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S600. Gene #80: 'xq loss' 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
XQ LOSS MUTATED	38	21	19	44	48	6
XQ LOSS WILD-TYPE	140	222	178	136	136	52

Figure S600. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0096

Table S601. Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	306	422	297
XQ LOSS MUTATED	25	83	65
XQ LOSS WILD-TYPE	281	339	232

Figure S601. Get High-res Image Gene #80: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtypes file = BRCA-TP.transferedmergedcluster.txt
Number of patients = 1044
Number of significantly arm-level cnvs = 80
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, 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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