Correlation between copy number variations of arm-level result and molecular subtypes

Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

02 April 2015 | analyses__2015_04_02

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1N58KD4

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 82 arm-level events and 10 molecular subtypes across 882 patients, 606 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 606 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
3p gain	102 (12%)	780	0.00109 (0.0018)	0.00824 (0.0122)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
3q gain	158 (18%)	724	0.00712 (0.0107)	0.0317 (0.0442)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
17p gain	197 (22%)	685	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
17q gain	222 (25%)	660	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
20q gain	237 (27%)	645	0.019 (0.0272)	0.0483 (0.0656)	1e-05 (2.07e-05)	5e-05 (9.69e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	4e-05 (7.79e-05)	1e-05 (2.07e-05)	0.00825 (0.0122)	0.00999 (0.0147)
xp gain	124 (14%)	758	0.00394 (0.00608)	0.00277 (0.00436)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
xq gain	125 (14%)	757	0.00014 (0.000256)	7e-05 (0.000132)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
1p loss	145 (16%)	737	0.00122 (0.002)	0.0127 (0.0185)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
1q loss	110 (12%)	772	0.00816 (0.0121)	0.00783 (0.0117)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
2p loss	65 (7%)	817	1e-05 (2.07e-05)	0.00031 (0.000545)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
2q loss	63 (7%)	819	7e-05 (0.000132)	6e-05 (0.000115)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
3p loss	412 (47%)	470	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
9p loss	192 (22%)	690	0.0112 (0.0164)	0.0211 (0.03)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00014 (0.000256)	0.00023 (0.000413)
9q loss	195 (22%)	687	0.0227 (0.0322)	0.0383 (0.0527)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	6e-05 (0.000115)	0.00033 (0.000577)
13q loss	137 (16%)	745	0.00292 (0.00457)	0.0115 (0.0168)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00067 (0.00113)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
14q loss	265 (30%)	617	7e-05 (0.000132)	8e-05 (0.000149)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
17p loss	110 (12%)	772	0.00092 (0.00154)	0.00294 (0.00459)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
17q loss	82 (9%)	800	0.0002 (0.000361)	0.00035 (0.000611)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
21q loss	133 (15%)	749	0.0157 (0.0227)	0.0239 (0.0338)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
12p gain	252 (29%)	630	0.0175 (0.0252)	0.0629 (0.0828)	1e-05 (2.07e-05)	3e-05 (5.94e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	8e-05 (0.000149)	4e-05 (7.79e-05)
12q gain	256 (29%)	626	0.0181 (0.026)	0.0626 (0.0825)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	3e-05 (5.94e-05)	7e-05 (0.000132)	3e-05 (5.94e-05)
20p gain	233 (26%)	649	0.0383 (0.0527)	0.076 (0.098)	1e-05 (2.07e-05)	0.0001 (0.000185)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	6e-05 (0.000115)	2e-05 (4.09e-05)	0.00576 (0.00868)	0.0054 (0.0082)
6p loss	172 (20%)	710	0.00236 (0.00374)	0.00358 (0.00555)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.0982 (0.125)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
6q loss	206 (23%)	676	0.00268 (0.00423)	0.00355 (0.00551)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.695 (0.749)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
22q loss	107 (12%)	775	0.00568 (0.00859)	0.0367 (0.0507)	4e-05 (7.79e-05)	0.00026 (0.000462)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	4e-05 (7.79e-05)	0.417 (0.47)	0.00163 (0.00264)	1e-05 (2.07e-05)
4p gain	46 (5%)	836	0.16 (0.2)	0.418 (0.47)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	2e-05 (4.09e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
4q gain	46 (5%)	836	0.295 (0.342)	0.649 (0.703)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
5p gain	237 (27%)	645	0.543 (0.595)	0.604 (0.657)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
5q gain	248 (28%)	634	0.164 (0.204)	0.21 (0.255)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
7p gain	368 (42%)	514	0.0917 (0.117)	0.109 (0.138)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
7q gain	370 (42%)	512	0.0908 (0.116)	0.11 (0.139)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
8q gain	99 (11%)	783	0.0612 (0.081)	0.243 (0.289)	1e-05 (2.07e-05)	0.00581 (0.00874)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.0192 (0.0274)	0.00012 (0.000221)	0.00066 (0.00112)	0.00023 (0.000413)
14q gain	39 (4%)	843	0.743 (0.797)	0.747 (0.801)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00051 (0.000871)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
16p gain	281 (32%)	601	0.0602 (0.0798)	0.0671 (0.0878)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
16q gain	268 (30%)	614	0.063 (0.0828)	0.059 (0.0787)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
18p gain	54 (6%)	828	0.492 (0.545)	0.749 (0.802)	0.00203 (0.00325)	0.00016 (0.00029)	0.00011 (0.000203)	3e-05 (5.94e-05)	0.0249 (0.0352)	1e-05 (2.07e-05)	0.00436 (0.0067)	0.0005 (0.000856)
18q gain	50 (6%)	832	0.527 (0.579)	0.776 (0.829)	0.00281 (0.00441)	0.00028 (0.000495)	3e-05 (5.94e-05)	2e-05 (4.09e-05)	0.0359 (0.0497)	1e-05 (2.07e-05)	0.00036 (0.000627)	3e-05 (5.94e-05)
19q gain	78 (9%)	804	0.0383 (0.0527)	0.065 (0.0851)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.252 (0.299)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
3q loss	124 (14%)	758	0.0852 (0.109)	0.0601 (0.0798)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	3e-05 (5.94e-05)	0.00014 (0.000256)
4p loss	98 (11%)	784	0.575 (0.626)	0.483 (0.537)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00056 (0.000955)	1e-05 (2.07e-05)	0.00089 (0.00149)	1e-05 (2.07e-05)
4q loss	92 (10%)	790	0.49 (0.544)	0.624 (0.678)	1e-05 (2.07e-05)	0.00089 (0.00149)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00332 (0.00518)	1e-05 (2.07e-05)	0.00057 (0.00097)	3e-05 (5.94e-05)
5p loss	24 (3%)	858			7e-05 (0.000132)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00213 (0.0034)	1e-05 (2.07e-05)	6e-05 (0.000115)	1e-05 (2.07e-05)
5q loss	22 (2%)	860			3e-05 (5.94e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00528 (0.00803)	1e-05 (2.07e-05)	9e-05 (0.000167)	2e-05 (4.09e-05)
8p loss	164 (19%)	718	0.285 (0.333)	0.278 (0.326)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
8q loss	87 (10%)	795	0.835 (0.887)	0.504 (0.557)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00385 (0.00596)	4e-05 (7.79e-05)	0.00025 (0.000447)	0.00038 (0.00066)
10p loss	131 (15%)	751	0.26 (0.308)	0.358 (0.41)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	9e-05 (0.000167)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
11p loss	43 (5%)	839	0.0348 (0.0484)	0.0709 (0.0923)	6e-05 (0.000115)	0.0298 (0.0417)	0.00031 (0.000545)	3e-05 (5.94e-05)	0.0484 (0.0656)	0.199 (0.244)	0.00025 (0.000447)	0.00011 (0.000203)
18p loss	142 (16%)	740	0.228 (0.273)	0.406 (0.459)	1e-05 (2.07e-05)	0.0311 (0.0434)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	8e-05 (0.000149)	0.0048 (0.00734)	0.00112 (0.00184)	0.00026 (0.000462)
18q loss	149 (17%)	733	0.163 (0.202)	0.353 (0.405)	1e-05 (2.07e-05)	0.0465 (0.0632)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00048 (0.000825)	0.00193 (0.0031)	0.00041 (0.000709)	2e-05 (4.09e-05)
xp loss	118 (13%)	764	0.0542 (0.0727)	0.0806 (0.104)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
xq loss	116 (13%)	766	0.0731 (0.0947)	0.11 (0.139)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
8p gain	67 (8%)	815	0.294 (0.341)	0.472 (0.525)	1e-05 (2.07e-05)	0.00093 (0.00155)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.203 (0.248)	3e-05 (5.94e-05)	0.00028 (0.000495)	1e-05 (2.07e-05)
9p gain	26 (3%)	856	0.0349 (0.0484)	0.0722 (0.0937)	0.0758 (0.0979)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.213 (0.258)	1e-05 (2.07e-05)	0.00113 (0.00186)	7e-05 (0.000132)
9q gain	24 (3%)	858			0.00888 (0.0131)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.293 (0.34)	1e-05 (2.07e-05)	0.00039 (0.000676)	3e-05 (5.94e-05)
11p gain	57 (6%)	825	0.291 (0.339)	0.813 (0.864)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.327 (0.376)	1e-05 (2.07e-05)	5e-05 (9.69e-05)	1e-05 (2.07e-05)
11q gain	55 (6%)	827	0.408 (0.46)	0.913 (0.957)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.224 (0.269)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
15q gain	52 (6%)	830	0.869 (0.917)	0.553 (0.605)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.181 (0.223)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
19p gain	75 (9%)	807	0.15 (0.188)	0.216 (0.261)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.471 (0.525)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
22q gain	64 (7%)	818	0.282 (0.329)	0.465 (0.519)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.943 (0.985)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
10q loss	156 (18%)	726	0.203 (0.248)	0.242 (0.288)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.109 (0.138)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	1e-05 (2.07e-05)
15q loss	69 (8%)	813	0.209 (0.255)	0.265 (0.313)	1e-05 (2.07e-05)	0.85 (0.901)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.0271 (0.0381)	0.0423 (0.0579)	0.00413 (0.00635)	0.00588 (0.00883)
19q loss	22 (2%)	860			7e-05 (0.000132)	0.00125 (0.00205)	0.00261 (0.00412)	0.00047 (0.00081)	0.00464 (0.00711)	0.325 (0.375)	0.0266 (0.0374)	0.0153 (0.0222)
1q gain	68 (8%)	814	0.549 (0.601)	0.695 (0.749)	1e-05 (2.07e-05)	0.15 (0.188)	1e-05 (2.07e-05)	1e-05 (2.07e-05)	0.00102 (0.00169)	1e-05 (2.07e-05)	0.173 (0.214)	0.00167 (0.0027)
2q gain	127 (14%)	755	0.525 (0.578)	0.329 (0.378)	1e-05 (2.07e-05)	0.0162 (0.0234)	0.0008 (0.00135)	1e-05 (2.07e-05)	0.21 (0.255)	0.00033 (0.000577)	0.00554 (0.0084)	0.0584 (0.0782)
11q loss	52 (6%)	830	0.157 (0.196)	0.303 (0.349)	1e-05 (2.07e-05)	0.191 (0.234)	3e-05 (5.94e-05)	1e-05 (2.07e-05)	0.0406 (0.0557)	0.376 (0.43)	0.00016 (0.00029)	0.00015 (0.000273)
16p loss	18 (2%)	864			0.0605 (0.0801)	7e-05 (0.000132)	0.00022 (0.000396)	0.00281 (0.00441)	0.0286 (0.0401)	0.0754 (0.0975)	0.00094 (0.00156)	0.00163 (0.00264)
16q loss	28 (3%)	854			0.00098 (0.00163)	0.00884 (0.0131)	0.0049 (0.00748)	0.0007 (0.00118)	0.0672 (0.0878)	0.0631 (0.0828)	0.0408 (0.0559)	0.0137 (0.0199)
19p loss	27 (3%)	855			4e-05 (7.79e-05)	0.00129 (0.00211)	0.00086 (0.00145)	0.00033 (0.000577)	0.0542 (0.0727)	0.632 (0.686)	0.004 (0.00617)	0.00252 (0.00399)
20p loss	12 (1%)	870			0.668 (0.723)	0.00573 (0.00865)	0.0021 (0.00336)	0.0236 (0.0334)	0.269 (0.317)	0.00714 (0.0107)	0.00109 (0.0018)	0.00519 (0.00791)
20q loss	6 (1%)	876			0.46 (0.514)	0.00729 (0.0109)	0.0224 (0.0318)	0.0212 (0.0302)	0.878 (0.924)	0.0101 (0.0148)	0.00811 (0.0121)	0.00138 (0.00225)
2p gain	119 (13%)	763	0.492 (0.545)	0.565 (0.617)	1e-05 (2.07e-05)	0.0523 (0.0706)	0.00049 (0.000841)	4e-05 (7.79e-05)	0.168 (0.208)	0.00065 (0.0011)	0.0187 (0.0269)	0.0597 (0.0794)
1p gain	30 (3%)	852	0.867 (0.917)	0.915 (0.959)	8e-05 (0.000149)	0.0529 (0.0712)	0.00015 (0.000273)	1e-05 (2.07e-05)	0.1 (0.127)	0.00346 (0.00538)	0.155 (0.194)	0.509 (0.562)
10p gain	30 (3%)	852	0.16 (0.2)	0.421 (0.472)	1e-05 (2.07e-05)	0.0156 (0.0226)	0.00146 (0.00238)	0.00192 (0.00309)	0.571 (0.623)	0.695 (0.749)	0.295 (0.342)	0.291 (0.339)
13q gain	53 (6%)	829	0.227 (0.272)	0.298 (0.344)	0.0578 (0.0774)	0.0614 (0.081)	0.0173 (0.0249)	0.0495 (0.0669)	0.0119 (0.0174)	0.00223 (0.00355)	0.402 (0.456)	0.135 (0.17)
21q gain	73 (8%)	809	0.399 (0.454)	0.45 (0.503)	1e-05 (2.07e-05)	0.406 (0.459)	0.00027 (0.000479)	0.0018 (0.00291)	0.0133 (0.0194)	0.22 (0.266)	0.958 (1)	0.211 (0.256)
6p gain	21 (2%)	861			0.068 (0.0887)	0.534 (0.586)	0.937 (0.98)	0.00233 (0.0037)	0.4 (0.454)	0.0915 (0.117)	0.0455 (0.0621)	0.00185 (0.00298)
10q gain	23 (3%)	859	0.0508 (0.0687)	0.117 (0.148)	0.00046 (0.000794)	0.165 (0.204)	0.0456 (0.0621)	0.0449 (0.0613)	0.524 (0.577)	0.841 (0.892)	0.853 (0.903)	0.699 (0.753)
6q gain	16 (2%)	866			0.0777 (0.1)	0.264 (0.313)	0.876 (0.923)	0.0346 (0.0482)	0.806 (0.859)	0.273 (0.321)	0.0712 (0.0925)	0.0585 (0.0782)
12q loss	4 (0%)	878			0.0221 (0.0314)		0.39 (0.445)	0.896 (0.941)	0.275 (0.322)	0.708 (0.761)
7p loss	4 (0%)	878			0.399 (0.454)	0.782 (0.834)	0.207 (0.253)	0.181 (0.223)	0.222 (0.267)	0.234 (0.28)	0.265 (0.313)	0.44 (0.493)
7q loss	4 (0%)	878			0.4 (0.454)	0.779 (0.832)	0.211 (0.255)	0.18 (0.223)	0.222 (0.267)	0.233 (0.278)	0.266 (0.313)	0.446 (0.5)
12p loss	7 (1%)	875			0.189 (0.233)	0.108 (0.138)	1 (1.00)	0.382 (0.436)	0.893 (0.939)	0.286 (0.334)	0.148 (0.186)	0.261 (0.309)

'1p gain' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00015

Table S1. Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
1P GAIN MUTATED	3	5	22
1P GAIN WILD-TYPE	279	305	268

Figure S1. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00027

Table S2. Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
1P GAIN MUTATED	3	17	5	4
1P GAIN WILD-TYPE	116	178	292	264

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S3. Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
1P GAIN MUTATED	1	8	1	16	3	0
1P GAIN WILD-TYPE	87	137	206	143	108	169

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.0054

Table S4. Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
1P GAIN MUTATED	1	28	1
1P GAIN WILD-TYPE	76	553	205

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S5. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
1Q GAIN MUTATED	6	16	46
1Q GAIN WILD-TYPE	276	294	244

Figure S5. 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 = 2.1e-05

Table S6. Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
1Q GAIN MUTATED	3	31	20	12
1Q GAIN WILD-TYPE	116	164	277	256

Figure S6. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S7. Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
1Q GAIN MUTATED	0	18	15	27	6	0
1Q GAIN WILD-TYPE	88	127	192	132	105	169

Figure S7. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00102 (Fisher's exact test), Q value = 0.0017

Table S8. Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
1Q GAIN MUTATED	12	17	37
1Q GAIN WILD-TYPE	316	175	307

Figure S8. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S9. Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
1Q GAIN MUTATED	0	65	1
1Q GAIN WILD-TYPE	77	516	205

Figure S9. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.0027

Table S10. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
1Q GAIN MUTATED	0	2	12	10	0
1Q GAIN WILD-TYPE	50	87	82	122	46

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S11. Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
2P GAIN MUTATED	32	6	81
2P GAIN WILD-TYPE	250	304	209

Figure S11. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #3: 'CN_CNMF'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.00084

Table S12. Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
2P GAIN MUTATED	5	39	37	37
2P GAIN WILD-TYPE	114	156	260	231

Figure S12. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S13. Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
2P GAIN MUTATED	1	19	20	34	17	27
2P GAIN WILD-TYPE	87	126	187	125	94	142

Figure S13. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00065 (Fisher's exact test), Q value = 0.0011

Table S14. Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
2P GAIN MUTATED	1	87	31
2P GAIN WILD-TYPE	76	494	175

Figure S14. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.027

Table S15. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
2P GAIN MUTATED	20	3	14	18
2P GAIN WILD-TYPE	133	67	49	107

Figure S15. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S16. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
2Q GAIN MUTATED	35	11	81
2Q GAIN WILD-TYPE	247	299	209

Figure S16. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.023

Table S17. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
2Q GAIN MUTATED	9	44	39
2Q GAIN WILD-TYPE	119	259	182

Figure S17. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0013

Table S18. Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
2Q GAIN MUTATED	5	38	42	42
2Q GAIN WILD-TYPE	114	157	255	226

Figure S18. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S19. Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
2Q GAIN MUTATED	1	20	20	34	21	31
2Q GAIN WILD-TYPE	87	125	187	125	90	138

Figure S19. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00058

Table S20. Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
2Q GAIN MUTATED	1	91	34
2Q GAIN WILD-TYPE	76	490	172

Figure S20. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00554 (Fisher's exact test), Q value = 0.0084

Table S21. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
2Q GAIN MUTATED	23	3	16	19
2Q GAIN WILD-TYPE	130	67	47	106

Figure S21. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MRNA_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0018

Table S22. Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
3P GAIN MUTATED	0	2	2	6
3P GAIN WILD-TYPE	33	22	10	11

Figure S22. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00824 (Fisher's exact test), Q value = 0.012

Table S23. Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
3P GAIN MUTATED	0	2	6	0	2
3P GAIN WILD-TYPE	20	22	12	13	9

Figure S23. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S24. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
3P GAIN MUTATED	85	3	14
3P GAIN WILD-TYPE	197	307	276

Figure S24. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S25. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
3P GAIN MUTATED	16	7	65
3P GAIN WILD-TYPE	112	296	156

Figure S25. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S26. Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
3P GAIN MUTATED	14	12	2	74
3P GAIN WILD-TYPE	105	183	295	194

Figure S26. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S27. Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
3P GAIN MUTATED	12	15	0	9	2	64
3P GAIN WILD-TYPE	76	130	207	150	109	105

Figure S27. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S28. Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
3P GAIN MUTATED	87	10	5
3P GAIN WILD-TYPE	241	182	339

Figure S28. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S29. Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
3P GAIN MUTATED	11	23	68
3P GAIN WILD-TYPE	66	558	138

Figure S29. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S30. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
3P GAIN MUTATED	46	7	6	3
3P GAIN WILD-TYPE	107	63	57	122

Figure S30. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S31. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
3P GAIN MUTATED	17	27	9	3	6
3P GAIN WILD-TYPE	33	62	85	129	40

Figure S31. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00712 (Fisher's exact test), Q value = 0.011

Table S32. Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
3Q GAIN MUTATED	1	7	2	6
3Q GAIN WILD-TYPE	32	17	10	11

Figure S32. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0317 (Fisher's exact test), Q value = 0.044

Table S33. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
3Q GAIN MUTATED	1	7	6	0	2
3Q GAIN WILD-TYPE	19	17	12	13	9

Figure S33. 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 = 2.1e-05

Table S34. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
3Q GAIN MUTATED	101	7	50
3Q GAIN WILD-TYPE	181	303	240

Figure S34. 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 = 2.1e-05

Table S35. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
3Q GAIN MUTATED	17	28	85
3Q GAIN WILD-TYPE	111	275	136

Figure S35. 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 = 2.1e-05

Table S36. Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
3Q GAIN MUTATED	15	34	14	95
3Q GAIN WILD-TYPE	104	161	283	173

Figure S36. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S37. Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
3Q GAIN MUTATED	12	25	10	31	4	76
3Q GAIN WILD-TYPE	76	120	197	128	107	93

Figure S37. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S38. Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
3Q GAIN MUTATED	104	29	24
3Q GAIN WILD-TYPE	224	163	320

Figure S38. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S39. Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
3Q GAIN MUTATED	11	64	82
3Q GAIN WILD-TYPE	66	517	124

Figure S39. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S40. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
3Q GAIN MUTATED	58	7	13	8
3Q GAIN WILD-TYPE	95	63	50	117

Figure S40. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S41. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
3Q GAIN MUTATED	16	37	18	9	6
3Q GAIN WILD-TYPE	34	52	76	123	40

Figure S41. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S42. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
4P GAIN MUTATED	22	2	22
4P GAIN WILD-TYPE	260	308	268

Figure S42. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S43. Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
4P GAIN MUTATED	27	3	6
4P GAIN WILD-TYPE	101	300	215

Figure S43. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S44. Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
4P GAIN MUTATED	26	8	3	8
4P GAIN WILD-TYPE	93	187	294	260

Figure S44. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S45. Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
4P GAIN MUTATED	26	8	1	6	0	4
4P GAIN WILD-TYPE	62	137	206	153	111	165

Figure S45. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S46. Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
4P GAIN MUTATED	33	6	7
4P GAIN WILD-TYPE	295	186	337

Figure S46. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S47. Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
4P GAIN MUTATED	26	14	6
4P GAIN WILD-TYPE	51	567	200

Figure S47. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S48. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
4P GAIN MUTATED	5	20	3	2
4P GAIN WILD-TYPE	148	50	60	123

Figure S48. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S49. Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
4P GAIN MUTATED	1	4	4	2	19
4P GAIN WILD-TYPE	49	85	90	130	27

Figure S49. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S50. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
4Q GAIN MUTATED	22	2	22
4Q GAIN WILD-TYPE	260	308	268

Figure S50. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S51. Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
4Q GAIN MUTATED	27	4	6
4Q GAIN WILD-TYPE	101	299	215

Figure S51. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S52. Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
4Q GAIN MUTATED	27	7	4	7
4Q GAIN WILD-TYPE	92	188	293	261

Figure S52. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S53. Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
4Q GAIN MUTATED	27	6	1	6	1	4
4Q GAIN WILD-TYPE	61	139	206	153	110	165

Figure S53. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S54. Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
4Q GAIN MUTATED	33	6	7
4Q GAIN WILD-TYPE	295	186	337

Figure S54. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S55. Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
4Q GAIN MUTATED	27	13	6
4Q GAIN WILD-TYPE	50	568	200

Figure S55. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S56. Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
4Q GAIN MUTATED	5	21	2	2
4Q GAIN WILD-TYPE	148	49	61	123

Figure S56. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S57. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
4Q GAIN MUTATED	1	4	3	2	20
4Q GAIN WILD-TYPE	49	85	91	130	26

Figure S57. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S58. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
5P GAIN MUTATED	37	46	154
5P GAIN WILD-TYPE	245	264	136

Figure S58. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S59. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
5P GAIN MUTATED	21	111	21
5P GAIN WILD-TYPE	107	192	200

Figure S59. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S60. Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
5P GAIN MUTATED	17	85	104	29
5P GAIN WILD-TYPE	102	110	193	239

Figure S60. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S61. Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
5P GAIN MUTATED	11	29	77	75	31	12
5P GAIN WILD-TYPE	77	116	130	84	80	157

Figure S61. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S62. Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
5P GAIN MUTATED	38	56	139
5P GAIN WILD-TYPE	290	136	205

Figure S62. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S63. Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
5P GAIN MUTATED	10	204	19
5P GAIN WILD-TYPE	67	377	187

Figure S63. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S64. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
5P GAIN MUTATED	17	9	17	52
5P GAIN WILD-TYPE	136	61	46	73

Figure S64. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S65. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
5P GAIN MUTATED	3	12	18	56	6
5P GAIN WILD-TYPE	47	77	76	76	40

Figure S65. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
5Q GAIN MUTATED	34	60	154
5Q GAIN WILD-TYPE	248	250	136

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

'5q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
5Q GAIN MUTATED	19	122	20
5Q GAIN WILD-TYPE	109	181	201

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

'5q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
5Q GAIN MUTATED	16	83	118	29
5Q GAIN WILD-TYPE	103	112	179	239

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

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S69. Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
5Q GAIN MUTATED	11	27	86	76	36	10
5Q GAIN WILD-TYPE	77	118	121	83	75	159

Figure S69. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S70. Gene #10: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
5Q GAIN MUTATED	36	57	149
5Q GAIN WILD-TYPE	292	135	195

Figure S70. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S71. Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
5Q GAIN MUTATED	10	213	19
5Q GAIN WILD-TYPE	67	368	187

Figure S71. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S72. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
5Q GAIN MUTATED	17	8	14	52
5Q GAIN WILD-TYPE	136	62	49	73

Figure S72. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S73. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
5Q GAIN MUTATED	3	12	15	55	6
5Q GAIN WILD-TYPE	47	77	79	77	40

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

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00233 (Fisher's exact test), Q value = 0.0037

Table S74. Gene #11: '6p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
6P GAIN MUTATED	1	11	5	1	2	1
6P GAIN WILD-TYPE	87	134	202	158	109	168

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

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.062

Table S75. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
6P GAIN MUTATED	2	3	5	2
6P GAIN WILD-TYPE	151	67	58	123

Figure S75. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.003

Table S76. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
6P GAIN MUTATED	1	1	9	1	0
6P GAIN WILD-TYPE	49	88	85	131	46

Figure S76. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0346 (Fisher's exact test), Q value = 0.048

Table S77. Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
6Q GAIN MUTATED	1	8	4	1	1	1
6Q GAIN WILD-TYPE	87	137	203	158	110	168

Figure S77. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S78. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
7P GAIN MUTATED	190	41	137
7P GAIN WILD-TYPE	92	269	153

Figure S78. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S79. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
7P GAIN MUTATED	40	80	153
7P GAIN WILD-TYPE	88	223	68

Figure S79. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S80. Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
7P GAIN MUTATED	36	87	72	171
7P GAIN WILD-TYPE	83	108	225	97

Figure S80. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S81. Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
7P GAIN MUTATED	30	41	61	66	26	142
7P GAIN WILD-TYPE	58	104	146	93	85	27

Figure S81. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S82. Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
7P GAIN MUTATED	186	70	109
7P GAIN WILD-TYPE	142	122	235

Figure S82. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S83. Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
7P GAIN MUTATED	29	188	148
7P GAIN WILD-TYPE	48	393	58

Figure S83. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S84. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
7P GAIN MUTATED	107	24	26	38
7P GAIN WILD-TYPE	46	46	37	87

Figure S84. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S85. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
7P GAIN MUTATED	41	60	33	41	20
7P GAIN WILD-TYPE	9	29	61	91	26

Figure S85. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S86. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
7Q GAIN MUTATED	190	40	140
7Q GAIN WILD-TYPE	92	270	150

Figure S86. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S87. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
7Q GAIN MUTATED	40	84	153
7Q GAIN WILD-TYPE	88	219	68

Figure S87. 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 = 2.1e-05

Table S88. Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
7Q GAIN MUTATED	36	88	73	171
7Q GAIN WILD-TYPE	83	107	224	97

Figure S88. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S89. Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
7Q GAIN MUTATED	30	41	60	69	26	142
7Q GAIN WILD-TYPE	58	104	147	90	85	27

Figure S89. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S90. Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
7Q GAIN MUTATED	186	73	108
7Q GAIN WILD-TYPE	142	119	236

Figure S90. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S91. Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
7Q GAIN MUTATED	29	190	148
7Q GAIN WILD-TYPE	48	391	58

Figure S91. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S92. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
7Q GAIN MUTATED	107	24	26	37
7Q GAIN WILD-TYPE	46	46	37	88

Figure S92. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S93. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
7Q GAIN MUTATED	41	60	33	40	20
7Q GAIN WILD-TYPE	9	29	61	92	26

Figure S93. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S94. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
8P GAIN MUTATED	26	3	38
8P GAIN WILD-TYPE	256	307	252

Figure S94. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0015

Table S95. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
8P GAIN MUTATED	23	20	15
8P GAIN WILD-TYPE	105	283	206

Figure S95. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S96. Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
8P GAIN MUTATED	20	24	6	17
8P GAIN WILD-TYPE	99	171	291	251

Figure S96. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S97. Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
8P GAIN MUTATED	17	16	7	19	0	8
8P GAIN WILD-TYPE	71	129	200	140	111	161

Figure S97. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S98. Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
8P GAIN MUTATED	17	41	9
8P GAIN WILD-TYPE	60	540	197

Figure S98. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00049

Table S99. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
8P GAIN MUTATED	10	15	10	5
8P GAIN WILD-TYPE	143	55	53	120

Figure S99. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S100. Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
8P GAIN MUTATED	2	6	13	5	14
8P GAIN WILD-TYPE	48	83	81	127	32

Figure S100. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S101. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
8Q GAIN MUTATED	30	4	65
8Q GAIN WILD-TYPE	252	306	225

Figure S101. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.00581 (Fisher's exact test), Q value = 0.0087

Table S102. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
8Q GAIN MUTATED	25	35	17
8Q GAIN WILD-TYPE	103	268	204

Figure S102. 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 = 2.1e-05

Table S103. Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
8Q GAIN MUTATED	22	48	8	20
8Q GAIN WILD-TYPE	97	147	289	248

Figure S103. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S104. Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
8Q GAIN MUTATED	17	21	10	42	0	8
8Q GAIN WILD-TYPE	71	124	197	117	111	161

Figure S104. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.027

Table S105. Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
8Q GAIN MUTATED	33	33	32
8Q GAIN WILD-TYPE	295	159	312

Figure S105. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00022

Table S106. Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
8Q GAIN MUTATED	17	71	10
8Q GAIN WILD-TYPE	60	510	196

Figure S106. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0011

Table S107. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
8Q GAIN MUTATED	11	16	14	11
8Q GAIN WILD-TYPE	142	54	49	114

Figure S107. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00041

Table S108. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
8Q GAIN MUTATED	1	8	17	12	14
8Q GAIN WILD-TYPE	49	81	77	120	32

Figure S108. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.0349 (Fisher's exact test), Q value = 0.048

Table S109. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
9P GAIN MUTATED	0	1	2	0
9P GAIN WILD-TYPE	33	23	10	17

Figure S109. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S110. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
9P GAIN MUTATED	13	5	1
9P GAIN WILD-TYPE	115	298	220

Figure S110. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S111. Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
9P GAIN MUTATED	14	2	9	1
9P GAIN WILD-TYPE	105	193	288	267

Figure S111. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S112. Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
9P GAIN MUTATED	12	4	3	3	4	0
9P GAIN WILD-TYPE	76	141	204	156	107	169

Figure S112. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S113. Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
9P GAIN MUTATED	12	14	0
9P GAIN WILD-TYPE	65	567	206

Figure S113. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S114. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
9P GAIN MUTATED	1	8	3	3
9P GAIN WILD-TYPE	152	62	60	122

Figure S114. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S115. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
9P GAIN MUTATED	0	0	4	3	8
9P GAIN WILD-TYPE	50	89	90	129	38

Figure S115. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 0.00888 (Fisher's exact test), Q value = 0.013

Table S116. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
9Q GAIN MUTATED	12	2	10
9Q GAIN WILD-TYPE	270	308	280

Figure S116. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S117. Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
9Q GAIN MUTATED	14	5	1
9Q GAIN WILD-TYPE	114	298	220

Figure S117. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S118. Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
9Q GAIN MUTATED	13	4	6	1
9Q GAIN WILD-TYPE	106	191	291	267

Figure S118. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S119. Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
9Q GAIN MUTATED	12	5	1	3	3	0
9Q GAIN WILD-TYPE	76	140	206	156	108	169

Figure S119. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S120. Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
9Q GAIN MUTATED	12	12	0
9Q GAIN WILD-TYPE	65	569	206

Figure S120. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.00068

Table S121. Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
9Q GAIN MUTATED	1	8	3	2
9Q GAIN WILD-TYPE	152	62	60	123

Figure S121. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S122. Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
9Q GAIN MUTATED	0	0	4	2	8
9Q GAIN WILD-TYPE	50	89	90	130	38

Figure S122. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S123. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
10P GAIN MUTATED	8	1	21
10P GAIN WILD-TYPE	274	309	269

Figure S123. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.023

Table S124. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
10P GAIN MUTATED	9	9	3
10P GAIN WILD-TYPE	119	294	218

Figure S124. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 0.00146 (Fisher's exact test), Q value = 0.0024

Table S125. Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
10P GAIN MUTATED	6	14	3	7
10P GAIN WILD-TYPE	113	181	294	261

Figure S125. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00192 (Fisher's exact test), Q value = 0.0031

Table S126. Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
10P GAIN MUTATED	4	8	3	12	0	3
10P GAIN WILD-TYPE	84	137	204	147	111	166

Figure S126. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00079

Table S127. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
10Q GAIN MUTATED	7	1	15
10Q GAIN WILD-TYPE	275	309	275

Figure S127. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.062

Table S128. Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
10Q GAIN MUTATED	3	10	3	7
10Q GAIN WILD-TYPE	116	185	294	261

Figure S128. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0449 (Fisher's exact test), Q value = 0.061

Table S129. Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
10Q GAIN MUTATED	2	7	3	8	0	3
10Q GAIN WILD-TYPE	86	138	204	151	111	166

Figure S129. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S130. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
11P GAIN MUTATED	17	1	39
11P GAIN WILD-TYPE	265	309	251

Figure S130. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S131. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
11P GAIN MUTATED	23	15	4
11P GAIN WILD-TYPE	105	288	217

Figure S131. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S132. Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
11P GAIN MUTATED	22	15	13	7
11P GAIN WILD-TYPE	97	180	284	261

Figure S132. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S133. Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
11P GAIN MUTATED	19	10	9	14	4	1
11P GAIN WILD-TYPE	69	135	198	145	107	168

Figure S133. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S134. Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
11P GAIN MUTATED	18	33	6
11P GAIN WILD-TYPE	59	548	200

Figure S134. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 9.7e-05

Table S135. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
11P GAIN MUTATED	4	14	4	4
11P GAIN WILD-TYPE	149	56	59	121

Figure S135. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S136. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
11P GAIN MUTATED	0	3	4	5	14
11P GAIN WILD-TYPE	50	86	90	127	32

Figure S136. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S137. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
11Q GAIN MUTATED	16	1	38
11Q GAIN WILD-TYPE	266	309	252

Figure S137. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S138. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
11Q GAIN MUTATED	23	13	4
11Q GAIN WILD-TYPE	105	290	217

Figure S138. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S139. Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
11Q GAIN MUTATED	22	12	14	7
11Q GAIN WILD-TYPE	97	183	283	261

Figure S139. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S140. Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
11Q GAIN MUTATED	20	9	10	11	4	1
11Q GAIN WILD-TYPE	68	136	197	148	107	168

Figure S140. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S141. Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
11Q GAIN MUTATED	19	31	5
11Q GAIN WILD-TYPE	58	550	201

Figure S141. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S142. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
11Q GAIN MUTATED	4	15	3	4
11Q GAIN WILD-TYPE	149	55	60	121

Figure S142. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S143. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
11Q GAIN MUTATED	0	3	4	4	15
11Q GAIN WILD-TYPE	50	86	90	128	31

Figure S143. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.025

Table S144. Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
12P GAIN MUTATED	3	10	2	6
12P GAIN WILD-TYPE	30	14	10	11

Figure S144. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S145. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
12P GAIN MUTATED	115	32	105
12P GAIN WILD-TYPE	167	278	185

Figure S145. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S146. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
12P GAIN MUTATED	34	72	95
12P GAIN WILD-TYPE	94	231	126

Figure S146. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S147. Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
12P GAIN MUTATED	29	75	37	110
12P GAIN WILD-TYPE	90	120	260	158

Figure S147. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S148. Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
12P GAIN MUTATED	24	39	31	65	10	82
12P GAIN WILD-TYPE	64	106	176	94	101	87

Figure S148. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S149. Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
12P GAIN MUTATED	126	52	72
12P GAIN WILD-TYPE	202	140	272

Figure S149. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S150. Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
12P GAIN MUTATED	23	140	87
12P GAIN WILD-TYPE	54	441	119

Figure S150. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00015

Table S151. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
12P GAIN MUTATED	66	19	21	22
12P GAIN WILD-TYPE	87	51	42	103

Figure S151. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S152. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
12P GAIN MUTATED	15	44	30	23	16
12P GAIN WILD-TYPE	35	45	64	109	30

Figure S152. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.026

Table S153. Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
12Q GAIN MUTATED	3	10	2	6
12Q GAIN WILD-TYPE	30	14	10	11

Figure S153. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S154. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
12Q GAIN MUTATED	118	32	106
12Q GAIN WILD-TYPE	164	278	184

Figure S154. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S155. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
12Q GAIN MUTATED	37	72	95
12Q GAIN WILD-TYPE	91	231	126

Figure S155. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S156. Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
12Q GAIN MUTATED	31	77	37	110
12Q GAIN WILD-TYPE	88	118	260	158

Figure S156. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S157. Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
12Q GAIN MUTATED	26	40	31	66	10	82
12Q GAIN WILD-TYPE	62	105	176	93	101	87

Figure S157. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S158. Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
12Q GAIN MUTATED	128	53	73
12Q GAIN WILD-TYPE	200	139	271

Figure S158. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S159. Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
12Q GAIN MUTATED	25	142	87
12Q GAIN WILD-TYPE	52	439	119

Figure S159. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S160. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
12Q GAIN MUTATED	66	21	22	22
12Q GAIN WILD-TYPE	87	49	41	103

Figure S160. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'12q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S161. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
12Q GAIN MUTATED	15	44	30	24	18
12Q GAIN WILD-TYPE	35	45	64	108	28

Figure S161. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.025

Table S162. Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
13Q GAIN MUTATED	4	9	13	27
13Q GAIN WILD-TYPE	115	186	284	241

Figure S162. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0495 (Fisher's exact test), Q value = 0.067

Table S163. Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
13Q GAIN MUTATED	3	10	11	7	3	19
13Q GAIN WILD-TYPE	85	135	196	152	108	150

Figure S163. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.017

Table S164. Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
13Q GAIN MUTATED	30	9	13
13Q GAIN WILD-TYPE	298	183	331

Figure S164. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00223 (Fisher's exact test), Q value = 0.0036

Table S165. Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
13Q GAIN MUTATED	2	27	23
13Q GAIN WILD-TYPE	75	554	183

Figure S165. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S166. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
14Q GAIN MUTATED	20	1	18
14Q GAIN WILD-TYPE	262	309	272

Figure S166. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S167. Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
14Q GAIN MUTATED	28	5	0
14Q GAIN WILD-TYPE	100	298	221

Figure S167. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S168. Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
14Q GAIN MUTATED	27	8	3	1
14Q GAIN WILD-TYPE	92	187	294	267

Figure S168. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S169. Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
14Q GAIN MUTATED	25	6	3	4	1	0
14Q GAIN WILD-TYPE	63	139	204	155	110	169

Figure S169. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 0.00087

Table S170. Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
14Q GAIN MUTATED	26	3	9
14Q GAIN WILD-TYPE	302	189	335

Figure S170. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S171. Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
14Q GAIN MUTATED	25	13	0
14Q GAIN WILD-TYPE	52	568	206

Figure S171. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S172. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
14Q GAIN MUTATED	0	18	3	0
14Q GAIN WILD-TYPE	153	52	60	125

Figure S172. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S173. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
14Q GAIN MUTATED	0	0	4	0	17
14Q GAIN WILD-TYPE	50	89	90	132	29

Figure S173. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S174. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
15Q GAIN MUTATED	21	1	30
15Q GAIN WILD-TYPE	261	309	260

Figure S174. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S175. Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
15Q GAIN MUTATED	25	11	3
15Q GAIN WILD-TYPE	103	292	218

Figure S175. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S176. Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
15Q GAIN MUTATED	25	10	12	4
15Q GAIN WILD-TYPE	94	185	285	264

Figure S176. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S177. Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
15Q GAIN MUTATED	24	5	11	8	2	1
15Q GAIN WILD-TYPE	64	140	196	151	109	168

Figure S177. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S178. Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
15Q GAIN MUTATED	24	25	2
15Q GAIN WILD-TYPE	53	556	204

Figure S178. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S179. Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
15Q GAIN MUTATED	0	17	1	5
15Q GAIN WILD-TYPE	153	53	62	120

Figure S179. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S180. Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
15Q GAIN MUTATED	0	0	1	5	17
15Q GAIN WILD-TYPE	50	89	93	127	29

Figure S180. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S181. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
16P GAIN MUTATED	156	24	101
16P GAIN WILD-TYPE	126	286	189

Figure S181. 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 = 2.1e-05

Table S182. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
16P GAIN MUTATED	34	57	136
16P GAIN WILD-TYPE	94	246	85

Figure S182. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S183. Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
16P GAIN MUTATED	32	49	46	154
16P GAIN WILD-TYPE	87	146	251	114

Figure S183. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S184. Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
16P GAIN MUTATED	27	49	35	41	17	112
16P GAIN WILD-TYPE	61	96	172	118	94	57

Figure S184. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S185. Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
16P GAIN MUTATED	173	37	70
16P GAIN WILD-TYPE	155	155	274

Figure S185. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S186. Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
16P GAIN MUTATED	25	124	131
16P GAIN WILD-TYPE	52	457	75

Figure S186. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S187. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
16P GAIN MUTATED	94	21	19	26
16P GAIN WILD-TYPE	59	49	44	99

Figure S187. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S188. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
16P GAIN MUTATED	27	61	28	26	18
16P GAIN WILD-TYPE	23	28	66	106	28

Figure S188. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S189. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
16Q GAIN MUTATED	155	22	91
16Q GAIN WILD-TYPE	127	288	199

Figure S189. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S190. Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
16Q GAIN MUTATED	34	52	132
16Q GAIN WILD-TYPE	94	251	89

Figure S190. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S191. Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
16Q GAIN MUTATED	31	48	41	148
16Q GAIN WILD-TYPE	88	147	256	120

Figure S191. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S192. Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
16Q GAIN MUTATED	26	44	30	40	17	111
16Q GAIN WILD-TYPE	62	101	177	119	94	58

Figure S192. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S193. Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
16Q GAIN MUTATED	168	36	63
16Q GAIN WILD-TYPE	160	156	281

Figure S193. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S194. Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
16Q GAIN MUTATED	25	111	131
16Q GAIN WILD-TYPE	52	470	75

Figure S194. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S195. Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
16Q GAIN MUTATED	92	21	17	22
16Q GAIN WILD-TYPE	61	49	46	103

Figure S195. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S196. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
16Q GAIN MUTATED	26	61	24	23	18
16Q GAIN WILD-TYPE	24	28	70	109	28

Figure S196. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S197. Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
17P GAIN MUTATED	1	0	2	11
17P GAIN WILD-TYPE	32	24	10	6

Figure S197. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S198. Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17P GAIN MUTATED	1	0	12	0	1
17P GAIN WILD-TYPE	19	24	6	13	10

Figure S198. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S199. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
17P GAIN MUTATED	164	7	26
17P GAIN WILD-TYPE	118	303	264

Figure S199. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S200. Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
17P GAIN MUTATED	15	12	152
17P GAIN WILD-TYPE	113	291	69

Figure S200. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S201. Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
17P GAIN MUTATED	5	14	9	169
17P GAIN WILD-TYPE	114	181	288	99

Figure S201. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S202. Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
17P GAIN MUTATED	1	32	7	9	1	147
17P GAIN WILD-TYPE	87	113	200	150	110	22

Figure S202. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S203. Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
17P GAIN MUTATED	165	19	12
17P GAIN WILD-TYPE	163	173	332

Figure S203. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S204. Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
17P GAIN MUTATED	0	45	151
17P GAIN WILD-TYPE	77	536	55

Figure S204. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S205. Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
17P GAIN MUTATED	109	5	14	3
17P GAIN WILD-TYPE	44	65	49	122

Figure S205. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S206. Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
17P GAIN MUTATED	42	63	23	3	0
17P GAIN WILD-TYPE	8	26	71	129	46

Figure S206. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S207. Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
17Q GAIN MUTATED	1	1	2	12
17Q GAIN WILD-TYPE	32	23	10	5

Figure S207. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S208. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17Q GAIN MUTATED	1	1	13	0	1
17Q GAIN WILD-TYPE	19	23	5	13	10

Figure S208. 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 = 2.1e-05

Table S209. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
17Q GAIN MUTATED	170	13	39
17Q GAIN WILD-TYPE	112	297	251

Figure S209. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S210. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
17Q GAIN MUTATED	17	18	165
17Q GAIN WILD-TYPE	111	285	56

Figure S210. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S211. Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
17Q GAIN MUTATED	7	18	10	187
17Q GAIN WILD-TYPE	112	177	287	81

Figure S211. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S212. Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
17Q GAIN MUTATED	1	49	9	13	1	149
17Q GAIN WILD-TYPE	87	96	198	146	110	20

Figure S212. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S213. Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
17Q GAIN MUTATED	178	30	13
17Q GAIN WILD-TYPE	150	162	331

Figure S213. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S214. Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
17Q GAIN MUTATED	0	61	160
17Q GAIN WILD-TYPE	77	520	46

Figure S214. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S215. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
17Q GAIN MUTATED	117	5	23	3
17Q GAIN WILD-TYPE	36	65	40	122

Figure S215. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S216. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
17Q GAIN MUTATED	44	66	35	3	0
17Q GAIN WILD-TYPE	6	23	59	129	46

Figure S216. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0033

Table S217. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
18P GAIN MUTATED	17	9	28
18P GAIN WILD-TYPE	265	301	262

Figure S217. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00029

Table S218. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
18P GAIN MUTATED	19	12	9
18P GAIN WILD-TYPE	109	291	212

Figure S218. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 2e-04

Table S219. Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
18P GAIN MUTATED	20	9	14	11
18P GAIN WILD-TYPE	99	186	283	257

Figure S219. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S220. Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
18P GAIN MUTATED	18	6	10	4	8	8
18P GAIN WILD-TYPE	70	139	197	155	103	161

Figure S220. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 0.0249 (Fisher's exact test), Q value = 0.035

Table S221. Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
18P GAIN MUTATED	29	6	18
18P GAIN WILD-TYPE	299	186	326

Figure S221. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S222. Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
18P GAIN MUTATED	17	28	8
18P GAIN WILD-TYPE	60	553	198

Figure S222. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00436 (Fisher's exact test), Q value = 0.0067

Table S223. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
18P GAIN MUTATED	8	14	3	9
18P GAIN WILD-TYPE	145	56	60	116

Figure S223. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.00086

Table S224. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
18P GAIN MUTATED	3	5	5	8	13
18P GAIN WILD-TYPE	47	84	89	124	33

Figure S224. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.0044

Table S225. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
18Q GAIN MUTATED	16	8	26
18Q GAIN WILD-TYPE	266	302	264

Figure S225. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00049

Table S226. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
18Q GAIN MUTATED	18	13	7
18Q GAIN WILD-TYPE	110	290	214

Figure S226. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S227. Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
18Q GAIN MUTATED	20	8	14	8
18Q GAIN WILD-TYPE	99	187	283	260

Figure S227. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S228. Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
18Q GAIN MUTATED	18	3	9	5	8	7
18Q GAIN WILD-TYPE	70	142	198	154	103	162

Figure S228. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.05

Table S229. Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
18Q GAIN MUTATED	26	5	18
18Q GAIN WILD-TYPE	302	187	326

Figure S229. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S230. Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
18Q GAIN MUTATED	17	25	7
18Q GAIN WILD-TYPE	60	556	199

Figure S230. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.00063

Table S231. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
18Q GAIN MUTATED	7	14	1	8
18Q GAIN WILD-TYPE	146	56	62	117

Figure S231. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S232. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
18Q GAIN MUTATED	2	5	2	8	13
18Q GAIN WILD-TYPE	48	84	92	124	33

Figure S232. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S233. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
19P GAIN MUTATED	17	1	57
19P GAIN WILD-TYPE	265	309	233

Figure S233. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S234. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
19P GAIN MUTATED	26	29	3
19P GAIN WILD-TYPE	102	274	218

Figure S234. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S235. Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
19P GAIN MUTATED	26	30	17	2
19P GAIN WILD-TYPE	93	165	280	266

Figure S235. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S236. Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
19P GAIN MUTATED	24	8	13	25	5	0
19P GAIN WILD-TYPE	64	137	194	134	106	169

Figure S236. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S237. Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
19P GAIN MUTATED	23	50	1
19P GAIN WILD-TYPE	54	531	205

Figure S237. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S238. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
19P GAIN MUTATED	1	15	2	12
19P GAIN WILD-TYPE	152	55	61	113

Figure S238. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S239. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
19P GAIN MUTATED	0	1	2	12	15
19P GAIN WILD-TYPE	50	88	92	120	31

Figure S239. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q gain' versus 'MRNA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.053

Table S240. Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
19Q GAIN MUTATED	1	3	3	0
19Q GAIN WILD-TYPE	32	21	9	17

Figure S240. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S241. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
19Q GAIN MUTATED	16	1	61
19Q GAIN WILD-TYPE	266	309	229

Figure S241. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S242. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
19Q GAIN MUTATED	24	31	3
19Q GAIN WILD-TYPE	104	272	218

Figure S242. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S243. Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
19Q GAIN MUTATED	25	32	18	2
19Q GAIN WILD-TYPE	94	163	279	266

Figure S243. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S244. Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
19Q GAIN MUTATED	23	7	14	28	5	0
19Q GAIN WILD-TYPE	65	138	193	131	106	169

Figure S244. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S245. Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
19Q GAIN MUTATED	22	53	1
19Q GAIN WILD-TYPE	55	528	205

Figure S245. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S246. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
19Q GAIN MUTATED	1	14	2	12
19Q GAIN WILD-TYPE	152	56	61	113

Figure S246. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S247. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
19Q GAIN MUTATED	0	1	2	12	14
19Q GAIN WILD-TYPE	50	88	92	120	32

Figure S247. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.053

Table S248. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
20P GAIN MUTATED	3	7	4	7
20P GAIN WILD-TYPE	30	17	8	10

Figure S248. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S249. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
20P GAIN MUTATED	111	13	109
20P GAIN WILD-TYPE	171	297	181

Figure S249. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00019

Table S250. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
20P GAIN MUTATED	35	60	83
20P GAIN WILD-TYPE	93	243	138

Figure S250. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S251. Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
20P GAIN MUTATED	31	82	27	93
20P GAIN WILD-TYPE	88	113	270	175

Figure S251. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S252. Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
20P GAIN MUTATED	26	32	26	66	8	75
20P GAIN WILD-TYPE	62	113	181	93	103	94

Figure S252. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S253. Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
20P GAIN MUTATED	115	49	68
20P GAIN WILD-TYPE	213	143	276

Figure S253. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S254. Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
20P GAIN MUTATED	25	126	81
20P GAIN WILD-TYPE	52	455	125

Figure S254. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.0087

Table S255. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
20P GAIN MUTATED	56	19	22	23
20P GAIN WILD-TYPE	97	51	41	102

Figure S255. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0054 (Fisher's exact test), Q value = 0.0082

Table S256. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
20P GAIN MUTATED	16	37	26	25	16
20P GAIN WILD-TYPE	34	52	68	107	30

Figure S256. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.027

Table S257. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
20Q GAIN MUTATED	3	8	5	7
20Q GAIN WILD-TYPE	30	16	7	10

Figure S257. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.066

Table S258. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
20Q GAIN MUTATED	2	8	8	1	4
20Q GAIN WILD-TYPE	18	16	10	12	7

Figure S258. 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 = 2.1e-05

Table S259. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
20Q GAIN MUTATED	110	15	112
20Q GAIN WILD-TYPE	172	295	178

Figure S259. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 9.7e-05

Table S260. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
20Q GAIN MUTATED	35	61	83
20Q GAIN WILD-TYPE	93	242	138

Figure S260. 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 = 2.1e-05

Table S261. Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
20Q GAIN MUTATED	32	85	27	93
20Q GAIN WILD-TYPE	87	110	270	175

Figure S261. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S262. Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
20Q GAIN MUTATED	26	34	26	69	8	74
20Q GAIN WILD-TYPE	62	111	181	90	103	95

Figure S262. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S263. Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
20Q GAIN MUTATED	116	51	69
20Q GAIN WILD-TYPE	212	141	275

Figure S263. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S264. Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
20Q GAIN MUTATED	25	130	81
20Q GAIN WILD-TYPE	52	451	125

Figure S264. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00825 (Fisher's exact test), Q value = 0.012

Table S265. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
20Q GAIN MUTATED	56	20	23	24
20Q GAIN WILD-TYPE	97	50	40	101

Figure S265. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.015

Table S266. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
20Q GAIN MUTATED	16	37	28	26	16
20Q GAIN WILD-TYPE	34	52	66	106	30

Figure S266. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S267. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
21Q GAIN MUTATED	19	4	50
21Q GAIN WILD-TYPE	263	306	240

Figure S267. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00048

Table S268. Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
21Q GAIN MUTATED	8	32	16	17
21Q GAIN WILD-TYPE	111	163	281	251

Figure S268. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0018 (Fisher's exact test), Q value = 0.0029

Table S269. Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
21Q GAIN MUTATED	5	7	14	28	6	13
21Q GAIN WILD-TYPE	83	138	193	131	105	156

Figure S269. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.019

Table S270. Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
21Q GAIN MUTATED	21	11	41
21Q GAIN WILD-TYPE	307	181	303

Figure S270. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S271. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
22Q GAIN MUTATED	19	4	41
22Q GAIN WILD-TYPE	263	306	249

Figure S271. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S272. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
22Q GAIN MUTATED	23	20	4
22Q GAIN WILD-TYPE	105	283	217

Figure S272. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S273. Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
22Q GAIN MUTATED	24	20	16	4
22Q GAIN WILD-TYPE	95	175	281	264

Figure S273. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S274. Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
22Q GAIN MUTATED	23	4	11	19	4	3
22Q GAIN WILD-TYPE	65	141	196	140	107	166

Figure S274. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S275. Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
22Q GAIN MUTATED	23	37	3
22Q GAIN WILD-TYPE	54	544	203

Figure S275. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S276. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
22Q GAIN MUTATED	3	16	3	3
22Q GAIN WILD-TYPE	150	54	60	122

Figure S276. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S277. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
22Q GAIN MUTATED	1	2	2	4	16
22Q GAIN WILD-TYPE	49	87	92	128	30

Figure S277. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 0.00394 (Fisher's exact test), Q value = 0.0061

Table S278. Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
XP GAIN MUTATED	2	1	1	7
XP GAIN WILD-TYPE	31	23	11	10

Figure S278. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00277 (Fisher's exact test), Q value = 0.0044

Table S279. Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
XP GAIN MUTATED	0	1	7	2	1
XP GAIN WILD-TYPE	20	23	11	11	10

Figure S279. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S280. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
XP GAIN MUTATED	93	4	27
XP GAIN WILD-TYPE	189	306	263

Figure S280. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S281. Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
XP GAIN MUTATED	14	10	77
XP GAIN WILD-TYPE	114	293	144

Figure S281. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S282. Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
XP GAIN MUTATED	11	19	8	86
XP GAIN WILD-TYPE	108	176	289	182

Figure S282. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S283. Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
XP GAIN MUTATED	8	15	4	16	4	77
XP GAIN WILD-TYPE	80	130	203	143	107	92

Figure S283. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S284. Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
XP GAIN MUTATED	92	12	20
XP GAIN WILD-TYPE	236	180	324

Figure S284. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S285. Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
XP GAIN MUTATED	7	37	80
XP GAIN WILD-TYPE	70	544	126

Figure S285. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S286. Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
XP GAIN MUTATED	54	9	3	6
XP GAIN WILD-TYPE	99	61	60	119

Figure S286. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S287. Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
XP GAIN MUTATED	16	33	12	5	6
XP GAIN WILD-TYPE	34	56	82	127	40

Figure S287. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00026

Table S288. Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
XQ GAIN MUTATED	2	0	1	8
XQ GAIN WILD-TYPE	31	24	11	9

Figure S288. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S289. Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
XQ GAIN MUTATED	0	0	8	2	1
XQ GAIN WILD-TYPE	20	24	10	11	10

Figure S289. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S290. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
XQ GAIN MUTATED	92	7	26
XQ GAIN WILD-TYPE	190	303	264

Figure S290. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S291. Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
XQ GAIN MUTATED	13	13	77
XQ GAIN WILD-TYPE	115	290	144

Figure S291. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S292. Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
XQ GAIN MUTATED	11	18	10	86
XQ GAIN WILD-TYPE	108	177	287	182

Figure S292. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S293. Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
XQ GAIN MUTATED	8	14	5	16	5	77
XQ GAIN WILD-TYPE	80	131	202	143	106	92

Figure S293. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S294. Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
XQ GAIN MUTATED	93	13	19
XQ GAIN WILD-TYPE	235	179	325

Figure S294. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S295. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
XQ GAIN MUTATED	7	37	81
XQ GAIN WILD-TYPE	70	544	125

Figure S295. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S296. Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
XQ GAIN MUTATED	54	9	3	7
XQ GAIN WILD-TYPE	99	61	60	118

Figure S296. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S297. Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
XQ GAIN MUTATED	16	33	11	7	6
XQ GAIN WILD-TYPE	34	56	83	125	40

Figure S297. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.002

Table S298. Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
1P LOSS MUTATED	2	3	7	2
1P LOSS WILD-TYPE	31	21	5	15

Figure S298. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.019

Table S299. Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
1P LOSS MUTATED	1	3	3	1	6
1P LOSS WILD-TYPE	19	21	15	12	5

Figure S299. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S300. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
1P LOSS MUTATED	79	7	59
1P LOSS WILD-TYPE	203	303	231

Figure S300. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S301. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
1P LOSS MUTATED	67	28	20
1P LOSS WILD-TYPE	61	275	201

Figure S301. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S302. Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
1P LOSS MUTATED	70	20	25	30
1P LOSS WILD-TYPE	49	175	272	238

Figure S302. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S303. Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
1P LOSS MUTATED	69	29	20	13	6	8
1P LOSS WILD-TYPE	19	116	187	146	105	161

Figure S303. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S304. Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
1P LOSS MUTATED	89	22	34
1P LOSS WILD-TYPE	239	170	310

Figure S304. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S305. Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
1P LOSS MUTATED	68	57	20
1P LOSS WILD-TYPE	9	524	186

Figure S305. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S306. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
1P LOSS MUTATED	12	41	9	10
1P LOSS WILD-TYPE	141	29	54	115

Figure S306. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S307. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
1P LOSS MUTATED	2	9	13	9	39
1P LOSS WILD-TYPE	48	80	81	123	7

Figure S307. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'MRNA_CNMF'

P value = 0.00816 (Fisher's exact test), Q value = 0.012

Table S308. Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
1Q LOSS MUTATED	2	1	5	1
1Q LOSS WILD-TYPE	31	23	7	16

Figure S308. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00783 (Fisher's exact test), Q value = 0.012

Table S309. Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
1Q LOSS MUTATED	1	1	1	1	5
1Q LOSS WILD-TYPE	19	23	17	12	6

Figure S309. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S310. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
1Q LOSS MUTATED	75	1	34
1Q LOSS WILD-TYPE	207	309	256

Figure S310. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S311. Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
1Q LOSS MUTATED	62	15	15
1Q LOSS WILD-TYPE	66	288	206

Figure S311. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S312. Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
1Q LOSS MUTATED	65	15	12	18
1Q LOSS WILD-TYPE	54	180	285	250

Figure S312. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S313. Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
1Q LOSS MUTATED	65	16	8	9	4	8
1Q LOSS WILD-TYPE	23	129	199	150	107	161

Figure S313. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S314. Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
1Q LOSS MUTATED	76	15	19
1Q LOSS WILD-TYPE	252	177	325

Figure S314. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S315. Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
1Q LOSS MUTATED	65	29	16
1Q LOSS WILD-TYPE	12	552	190

Figure S315. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S316. Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
1Q LOSS MUTATED	8	38	7	5
1Q LOSS WILD-TYPE	145	32	56	120

Figure S316. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S317. Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
1Q LOSS MUTATED	2	6	6	6	38
1Q LOSS WILD-TYPE	48	83	88	126	8

Figure S317. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S318. Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
2P LOSS MUTATED	0	1	6	0
2P LOSS WILD-TYPE	33	23	6	17

Figure S318. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00055

Table S319. Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
2P LOSS MUTATED	0	1	1	0	5
2P LOSS WILD-TYPE	20	23	17	13	6

Figure S319. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S320. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
2P LOSS MUTATED	53	0	12
2P LOSS WILD-TYPE	229	310	278

Figure S320. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S321. Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
2P LOSS MUTATED	52	3	2
2P LOSS WILD-TYPE	76	300	219

Figure S321. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S322. Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
2P LOSS MUTATED	60	2	0	3
2P LOSS WILD-TYPE	59	193	297	265

Figure S322. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S323. Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
2P LOSS MUTATED	58	5	0	2	0	0
2P LOSS WILD-TYPE	30	140	207	157	111	169

Figure S323. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S324. Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
2P LOSS MUTATED	59	3	3
2P LOSS WILD-TYPE	269	189	341

Figure S324. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S325. Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
2P LOSS MUTATED	58	5	2
2P LOSS WILD-TYPE	19	576	204

Figure S325. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S326. Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
2P LOSS MUTATED	1	36	0	1
2P LOSS WILD-TYPE	152	34	63	124

Figure S326. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S327. Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
2P LOSS MUTATED	0	1	1	1	35
2P LOSS WILD-TYPE	50	88	93	131	11

Figure S327. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q loss' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S328. Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
2Q LOSS MUTATED	0	1	5	0
2Q LOSS WILD-TYPE	33	23	7	17

Figure S328. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q loss' versus 'MRNA_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S329. Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
2Q LOSS MUTATED	0	1	0	0	5
2Q LOSS WILD-TYPE	20	23	18	13	6

Figure S329. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S330. Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
2Q LOSS MUTATED	52	0	11
2Q LOSS WILD-TYPE	230	310	279

Figure S330. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S331. Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
2Q LOSS MUTATED	53	2	1
2Q LOSS WILD-TYPE	75	301	220

Figure S331. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S332. Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
2Q LOSS MUTATED	59	3	0	1
2Q LOSS WILD-TYPE	60	192	297	267

Figure S332. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S333. Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
2Q LOSS MUTATED	58	3	0	2	0	0
2Q LOSS WILD-TYPE	30	142	207	157	111	169

Figure S333. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S334. Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
2Q LOSS MUTATED	57	2	4
2Q LOSS WILD-TYPE	271	190	340

Figure S334. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S335. Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
2Q LOSS MUTATED	58	4	1
2Q LOSS WILD-TYPE	19	577	205

Figure S335. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S336. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
2Q LOSS MUTATED	1	36	0	1
2Q LOSS WILD-TYPE	152	34	63	124

Figure S336. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S337. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
2Q LOSS MUTATED	0	1	1	1	35
2Q LOSS WILD-TYPE	50	88	93	131	11

Figure S337. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S338. Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
3P LOSS MUTATED	22	20	3	0
3P LOSS WILD-TYPE	11	4	9	17

Figure S338. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S339. Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
3P LOSS MUTATED	15	20	1	7	2
3P LOSS WILD-TYPE	5	4	17	6	9

Figure S339. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S340. Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
3P LOSS MUTATED	1	165	246
3P LOSS WILD-TYPE	281	145	44

Figure S340. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S341. Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
3P LOSS MUTATED	16	236	11
3P LOSS WILD-TYPE	112	67	210

Figure S341. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S342. Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
3P LOSS MUTATED	19	136	237	18
3P LOSS WILD-TYPE	100	59	60	250

Figure S342. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S343. Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
3P LOSS MUTATED	11	23	169	121	84	2
3P LOSS WILD-TYPE	77	122	38	38	27	167

Figure S343. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S344. Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
3P LOSS MUTATED	25	99	274
3P LOSS WILD-TYPE	303	93	70

Figure S344. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S345. Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
3P LOSS MUTATED	10	380	8
3P LOSS WILD-TYPE	67	201	198

Figure S345. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S346. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
3P LOSS MUTATED	7	7	15	94
3P LOSS WILD-TYPE	146	63	48	31

Figure S346. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S347. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
3P LOSS MUTATED	0	5	14	98	6
3P LOSS WILD-TYPE	50	84	80	34	40

Figure S347. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S348. Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
3Q LOSS MUTATED	1	34	89
3Q LOSS WILD-TYPE	281	276	201

Figure S348. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S349. Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
3Q LOSS MUTATED	11	62	4
3Q LOSS WILD-TYPE	117	241	217

Figure S349. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S350. Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
3Q LOSS MUTATED	13	48	58	5
3Q LOSS WILD-TYPE	106	147	239	263

Figure S350. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S351. Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
3Q LOSS MUTATED	9	9	58	33	14	1
3Q LOSS WILD-TYPE	79	136	149	126	97	168

Figure S351. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S352. Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
3Q LOSS MUTATED	13	25	82
3Q LOSS WILD-TYPE	315	167	262

Figure S352. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S353. Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
3Q LOSS MUTATED	9	108	3
3Q LOSS WILD-TYPE	68	473	203

Figure S353. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S354. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
3Q LOSS MUTATED	2	5	5	22
3Q LOSS WILD-TYPE	151	65	58	103

Figure S354. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00026

Table S355. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
3Q LOSS MUTATED	0	2	5	22	5
3Q LOSS WILD-TYPE	50	87	89	110	41

Figure S355. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S356. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
4P LOSS MUTATED	16	10	72
4P LOSS WILD-TYPE	266	300	218

Figure S356. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S357. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
4P LOSS MUTATED	15	51	9
4P LOSS WILD-TYPE	113	252	212

Figure S357. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S358. Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
4P LOSS MUTATED	4	40	35	18
4P LOSS WILD-TYPE	115	155	262	250

Figure S358. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S359. Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
4P LOSS MUTATED	0	29	23	31	13	1
4P LOSS WILD-TYPE	88	116	184	128	98	168

Figure S359. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.00095

Table S360. Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
4P LOSS MUTATED	21	32	43
4P LOSS WILD-TYPE	307	160	301

Figure S360. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S361. Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
4P LOSS MUTATED	0	86	10
4P LOSS WILD-TYPE	77	495	196

Figure S361. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0015

Table S362. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
4P LOSS MUTATED	6	4	13	15
4P LOSS WILD-TYPE	147	66	50	110

Figure S362. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S363. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
4P LOSS MUTATED	0	4	18	16	0
4P LOSS WILD-TYPE	50	85	76	116	46

Figure S363. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S364. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
4Q LOSS MUTATED	16	6	70
4Q LOSS WILD-TYPE	266	304	220

Figure S364. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 0.00089 (Fisher's exact test), Q value = 0.0015

Table S365. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
4Q LOSS MUTATED	15	45	11
4Q LOSS WILD-TYPE	113	258	210

Figure S365. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S366. Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
4Q LOSS MUTATED	4	40	29	19
4Q LOSS WILD-TYPE	115	155	268	249

Figure S366. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S367. Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
4Q LOSS MUTATED	0	30	20	31	10	1
4Q LOSS WILD-TYPE	88	115	187	128	101	168

Figure S367. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.0052

Table S368. Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
4Q LOSS MUTATED	22	31	38
4Q LOSS WILD-TYPE	306	161	306

Figure S368. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S369. Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
4Q LOSS MUTATED	0	81	10
4Q LOSS WILD-TYPE	77	500	196

Figure S369. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.00097

Table S370. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
4Q LOSS MUTATED	7	3	14	13
4Q LOSS WILD-TYPE	146	67	49	112

Figure S370. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S371. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
4Q LOSS MUTATED	0	4	18	15	0
4Q LOSS WILD-TYPE	50	85	76	117	46

Figure S371. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S372. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
5P LOSS MUTATED	17	1	6
5P LOSS WILD-TYPE	265	309	284

Figure S372. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S373. Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
5P LOSS MUTATED	19	2	2
5P LOSS WILD-TYPE	109	301	219

Figure S373. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S374. Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
5P LOSS MUTATED	13	9	0	2
5P LOSS WILD-TYPE	106	186	297	266

Figure S374. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S375. Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
5P LOSS MUTATED	11	9	0	3	0	1
5P LOSS WILD-TYPE	77	136	207	156	111	168

Figure S375. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.0034

Table S376. Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
5P LOSS MUTATED	14	8	2
5P LOSS WILD-TYPE	314	184	342

Figure S376. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S377. Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
5P LOSS MUTATED	11	12	1
5P LOSS WILD-TYPE	66	569	205

Figure S377. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S378. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
5P LOSS MUTATED	2	9	5	1
5P LOSS WILD-TYPE	151	61	58	124

Figure S378. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S379. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
5P LOSS MUTATED	0	1	7	1	8
5P LOSS WILD-TYPE	50	88	87	131	38

Figure S379. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S380. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
5Q LOSS MUTATED	16	0	6
5Q LOSS WILD-TYPE	266	310	284

Figure S380. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S381. Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
5Q LOSS MUTATED	19	1	2
5Q LOSS WILD-TYPE	109	302	219

Figure S381. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S382. Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
5Q LOSS MUTATED	13	8	0	1
5Q LOSS WILD-TYPE	106	187	297	267

Figure S382. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S383. Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
5Q LOSS MUTATED	11	8	0	2	0	1
5Q LOSS WILD-TYPE	77	137	207	157	111	168

Figure S383. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 0.00528 (Fisher's exact test), Q value = 0.008

Table S384. Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
5Q LOSS MUTATED	13	7	2
5Q LOSS WILD-TYPE	315	185	342

Figure S384. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S385. Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
5Q LOSS MUTATED	11	10	1
5Q LOSS WILD-TYPE	66	571	205

Figure S385. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00017

Table S386. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
5Q LOSS MUTATED	2	9	5	1
5Q LOSS WILD-TYPE	151	61	58	124

Figure S386. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S387. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
5Q LOSS MUTATED	0	1	7	1	8
5Q LOSS WILD-TYPE	50	88	87	131	38

Figure S387. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CNMF'

P value = 0.00236 (Fisher's exact test), Q value = 0.0037

Table S388. Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
6P LOSS MUTATED	4	10	6	1
6P LOSS WILD-TYPE	29	14	6	16

Figure S388. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.0055

Table S389. Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
6P LOSS MUTATED	3	10	1	1	6
6P LOSS WILD-TYPE	17	14	17	12	5

Figure S389. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S390. Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
6P LOSS MUTATED	65	2	105
6P LOSS WILD-TYPE	217	308	185

Figure S390. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S391. Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
6P LOSS MUTATED	63	47	12
6P LOSS WILD-TYPE	65	256	209

Figure S391. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S392. Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
6P LOSS MUTATED	65	63	27	15
6P LOSS WILD-TYPE	54	132	270	253

Figure S392. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S393. Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
6P LOSS MUTATED	61	20	24	51	8	6
6P LOSS WILD-TYPE	27	125	183	108	103	163

Figure S393. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S394. Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
6P LOSS MUTATED	61	92	15
6P LOSS WILD-TYPE	16	489	191

Figure S394. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S395. Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
6P LOSS MUTATED	8	38	12	14
6P LOSS WILD-TYPE	145	32	51	111

Figure S395. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S396. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
6P LOSS MUTATED	1	7	12	15	37
6P LOSS WILD-TYPE	49	82	82	117	9

Figure S396. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CNMF'

P value = 0.00268 (Fisher's exact test), Q value = 0.0042

Table S397. Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
6Q LOSS MUTATED	7	11	7	1
6Q LOSS WILD-TYPE	26	13	5	16

Figure S397. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00355 (Fisher's exact test), Q value = 0.0055

Table S398. Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
6Q LOSS MUTATED	4	11	1	3	7
6Q LOSS WILD-TYPE	16	13	17	10	4

Figure S398. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S399. Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
6Q LOSS MUTATED	66	2	138
6Q LOSS WILD-TYPE	216	308	152

Figure S399. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S400. Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
6Q LOSS MUTATED	65	63	16
6Q LOSS WILD-TYPE	63	240	205

Figure S400. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S401. Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
6Q LOSS MUTATED	66	65	51	22
6Q LOSS WILD-TYPE	53	130	246	246

Figure S401. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S402. Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
6Q LOSS MUTATED	61	28	35	53	22	5
6Q LOSS WILD-TYPE	27	117	172	106	89	164

Figure S402. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S403. Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
6Q LOSS MUTATED	61	122	19
6Q LOSS WILD-TYPE	16	459	187

Figure S403. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S404. Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
6Q LOSS MUTATED	10	39	13	22
6Q LOSS WILD-TYPE	143	31	50	103

Figure S404. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S405. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
6Q LOSS MUTATED	2	7	15	23	37
6Q LOSS WILD-TYPE	48	82	79	109	9

Figure S405. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S406. Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
8P LOSS MUTATED	25	39	100
8P LOSS WILD-TYPE	257	271	190

Figure S406. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S407. Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
8P LOSS MUTATED	18	73	8
8P LOSS WILD-TYPE	110	230	213

Figure S407. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S408. Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
8P LOSS MUTATED	19	61	71	12
8P LOSS WILD-TYPE	100	134	226	256

Figure S408. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S409. Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
8P LOSS MUTATED	16	14	56	51	23	3
8P LOSS WILD-TYPE	72	131	151	108	88	166

Figure S409. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S410. Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
8P LOSS MUTATED	28	43	90
8P LOSS WILD-TYPE	300	149	254

Figure S410. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S411. Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
8P LOSS MUTATED	15	140	6
8P LOSS WILD-TYPE	62	441	200

Figure S411. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S412. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
8P LOSS MUTATED	6	8	5	33
8P LOSS WILD-TYPE	147	62	58	92

Figure S412. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S413. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
8P LOSS MUTATED	1	3	7	35	6
8P LOSS WILD-TYPE	49	86	87	97	40

Figure S413. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S414. Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
8Q LOSS MUTATED	17	20	50
8Q LOSS WILD-TYPE	265	290	240

Figure S414. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S415. Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
8Q LOSS MUTATED	15	37	4
8Q LOSS WILD-TYPE	113	266	217

Figure S415. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S416. Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
8Q LOSS MUTATED	16	21	44	6
8Q LOSS WILD-TYPE	103	174	253	262

Figure S416. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S417. Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
8Q LOSS MUTATED	14	8	37	16	11	1
8Q LOSS WILD-TYPE	74	137	170	143	100	168

Figure S417. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.006

Table S418. Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
8Q LOSS MUTATED	19	23	44
8Q LOSS WILD-TYPE	309	169	300

Figure S418. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S419. Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
8Q LOSS MUTATED	13	68	5
8Q LOSS WILD-TYPE	64	513	201

Figure S419. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S420. Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
8Q LOSS MUTATED	2	7	3	17
8Q LOSS WILD-TYPE	151	63	60	108

Figure S420. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00038 (Fisher's exact test), Q value = 0.00066

Table S421. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
8Q LOSS MUTATED	0	2	3	18	6
8Q LOSS WILD-TYPE	50	87	91	114	40

Figure S421. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.016

Table S422. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
9P LOSS MUTATED	5	12	1	3
9P LOSS WILD-TYPE	28	12	11	14

Figure S422. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0211 (Fisher's exact test), Q value = 0.03

Table S423. Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
9P LOSS MUTATED	4	12	3	1	1
9P LOSS WILD-TYPE	16	12	15	12	10

Figure S423. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S424. Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
9P LOSS MUTATED	21	33	138
9P LOSS WILD-TYPE	261	277	152

Figure S424. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S425. Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
9P LOSS MUTATED	24	90	19
9P LOSS WILD-TYPE	104	213	202

Figure S425. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S426. Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
9P LOSS MUTATED	18	103	42	28
9P LOSS WILD-TYPE	101	92	255	240

Figure S426. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S427. Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
9P LOSS MUTATED	11	38	44	85	10	3
9P LOSS WILD-TYPE	77	107	163	74	101	166

Figure S427. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S428. Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
9P LOSS MUTATED	36	64	87
9P LOSS WILD-TYPE	292	128	257

Figure S428. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S429. Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
9P LOSS MUTATED	10	162	15
9P LOSS WILD-TYPE	67	419	191

Figure S429. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00026

Table S430. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
9P LOSS MUTATED	11	12	19	26
9P LOSS WILD-TYPE	142	58	44	99

Figure S430. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00041

Table S431. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
9P LOSS MUTATED	2	7	24	29	6
9P LOSS WILD-TYPE	48	82	70	103	40

Figure S431. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.032

Table S432. Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
9Q LOSS MUTATED	5	12	2	3
9Q LOSS WILD-TYPE	28	12	10	14

Figure S432. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.053

Table S433. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
9Q LOSS MUTATED	4	12	3	1	2
9Q LOSS WILD-TYPE	16	12	15	12	9

Figure S433. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S434. Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
9Q LOSS MUTATED	21	34	140
9Q LOSS WILD-TYPE	261	276	150

Figure S434. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S435. Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
9Q LOSS MUTATED	27	89	17
9Q LOSS WILD-TYPE	101	214	204

Figure S435. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S436. Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
9Q LOSS MUTATED	22	104	42	26
9Q LOSS WILD-TYPE	97	91	255	242

Figure S436. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S437. Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
9Q LOSS MUTATED	13	37	45	87	9	3
9Q LOSS WILD-TYPE	75	108	162	72	102	166

Figure S437. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S438. Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
9Q LOSS MUTATED	39	64	86
9Q LOSS WILD-TYPE	289	128	258

Figure S438. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S439. Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
9Q LOSS MUTATED	12	163	14
9Q LOSS WILD-TYPE	65	418	192

Figure S439. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S440. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
9Q LOSS MUTATED	11	14	19	27
9Q LOSS WILD-TYPE	142	56	44	98

Figure S440. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00058

Table S441. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
9Q LOSS MUTATED	2	7	24	30	8
9Q LOSS WILD-TYPE	48	82	70	102	38

Figure S441. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S442. Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
10P LOSS MUTATED	58	9	64
10P LOSS WILD-TYPE	224	301	226

Figure S442. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S443. Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
10P LOSS MUTATED	59	33	11
10P LOSS WILD-TYPE	69	270	210

Figure S443. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S444. Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
10P LOSS MUTATED	60	29	29	13
10P LOSS WILD-TYPE	59	166	268	255

Figure S444. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S445. Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
10P LOSS MUTATED	58	19	22	22	9	1
10P LOSS WILD-TYPE	30	126	185	137	102	168

Figure S445. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00017

Table S446. Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
10P LOSS MUTATED	68	29	32
10P LOSS WILD-TYPE	260	163	312

Figure S446. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S447. Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
10P LOSS MUTATED	58	65	6
10P LOSS WILD-TYPE	19	516	200

Figure S447. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S448. Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
10P LOSS MUTATED	3	36	9	11
10P LOSS WILD-TYPE	150	34	54	114

Figure S448. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S449. Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
10P LOSS MUTATED	1	1	12	11	34
10P LOSS WILD-TYPE	49	88	82	121	12

Figure S449. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S450. Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
10Q LOSS MUTATED	57	15	84
10Q LOSS WILD-TYPE	225	295	206

Figure S450. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S451. Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
10Q LOSS MUTATED	62	47	12
10Q LOSS WILD-TYPE	66	256	209

Figure S451. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S452. Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
10Q LOSS MUTATED	63	39	40	14
10Q LOSS WILD-TYPE	56	156	257	254

Figure S452. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S453. Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
10Q LOSS MUTATED	59	22	30	30	14	1
10Q LOSS WILD-TYPE	29	123	177	129	97	168

Figure S453. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S454. Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
10Q LOSS MUTATED	59	90	5
10Q LOSS WILD-TYPE	18	491	201

Figure S454. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S455. Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
10Q LOSS MUTATED	3	38	11	16
10Q LOSS WILD-TYPE	150	32	52	109

Figure S455. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S456. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
10Q LOSS MUTATED	1	1	15	16	35
10Q LOSS WILD-TYPE	49	88	79	116	11

Figure S456. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'MRNA_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.048

Table S457. Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
11P LOSS MUTATED	0	1	2	0
11P LOSS WILD-TYPE	33	23	10	17

Figure S457. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p loss' versus 'CN_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00011

Table S458. Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
11P LOSS MUTATED	14	4	25
11P LOSS WILD-TYPE	268	306	265

Figure S458. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.042

Table S459. Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
11P LOSS MUTATED	13	11	12
11P LOSS WILD-TYPE	115	292	209

Figure S459. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00055

Table S460. Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
11P LOSS MUTATED	12	14	4	13
11P LOSS WILD-TYPE	107	181	293	255

Figure S460. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S461. Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
11P LOSS MUTATED	8	18	4	9	1	3
11P LOSS WILD-TYPE	80	127	203	150	110	166

Figure S461. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 0.0484 (Fisher's exact test), Q value = 0.066

Table S462. Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
11P LOSS MUTATED	19	14	10
11P LOSS WILD-TYPE	309	178	334

Figure S462. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S463. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
11P LOSS MUTATED	6	8	10	2
11P LOSS WILD-TYPE	147	62	53	123

Figure S463. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 2e-04

Table S464. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
11P LOSS MUTATED	1	3	14	2	6
11P LOSS WILD-TYPE	49	86	80	130	40

Figure S464. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S465. Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
11Q LOSS MUTATED	15	3	34
11Q LOSS WILD-TYPE	267	307	256

Figure S465. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 5.9e-05

Table S466. Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
11Q LOSS MUTATED	11	19	4	18
11Q LOSS WILD-TYPE	108	176	293	250

Figure S466. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S467. Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
11Q LOSS MUTATED	7	23	4	14	1	3
11Q LOSS WILD-TYPE	81	122	203	145	110	166

Figure S467. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.056

Table S468. Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
11Q LOSS MUTATED	22	17	13
11Q LOSS WILD-TYPE	306	175	331

Figure S468. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00029

Table S469. Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
11Q LOSS MUTATED	9	7	12	2
11Q LOSS WILD-TYPE	144	63	51	123

Figure S469. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00027

Table S470. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
11Q LOSS MUTATED	1	6	15	2	6
11Q LOSS WILD-TYPE	49	83	79	130	40

Figure S470. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 0.0221 (Fisher's exact test), Q value = 0.031

Table S471. Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
12Q LOSS MUTATED	0	0	4
12Q LOSS WILD-TYPE	282	310	286

Figure S471. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'MRNA_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.0046

Table S472. Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
13Q LOSS MUTATED	0	6	3	1
13Q LOSS WILD-TYPE	33	18	9	16

Figure S472. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.017

Table S473. Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
13Q LOSS MUTATED	0	6	1	0	3
13Q LOSS WILD-TYPE	20	18	17	13	8

Figure S473. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S474. Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
13Q LOSS MUTATED	61	8	68
13Q LOSS WILD-TYPE	221	302	222

Figure S474. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S475. Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
13Q LOSS MUTATED	62	39	10
13Q LOSS WILD-TYPE	66	264	211

Figure S475. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S476. Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
13Q LOSS MUTATED	55	53	15	14
13Q LOSS WILD-TYPE	64	142	282	254

Figure S476. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S477. Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
13Q LOSS MUTATED	51	27	9	42	6	2
13Q LOSS WILD-TYPE	37	118	198	117	105	167

Figure S477. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0011

Table S478. Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
13Q LOSS MUTATED	64	37	34
13Q LOSS WILD-TYPE	264	155	310

Figure S478. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S479. Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
13Q LOSS MUTATED	50	75	10
13Q LOSS WILD-TYPE	27	506	196

Figure S479. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S480. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
13Q LOSS MUTATED	7	33	17	9
13Q LOSS WILD-TYPE	146	37	46	116

Figure S480. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S481. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
13Q LOSS MUTATED	1	4	19	11	31
13Q LOSS WILD-TYPE	49	85	75	121	15

Figure S481. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S482. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
14Q LOSS MUTATED	9	19	2	4
14Q LOSS WILD-TYPE	24	5	10	13

Figure S482. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00015

Table S483. Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
14Q LOSS MUTATED	4	19	4	5	2
14Q LOSS WILD-TYPE	16	5	14	8	9

Figure S483. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S484. Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
14Q LOSS MUTATED	33	76	156
14Q LOSS WILD-TYPE	249	234	134

Figure S484. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S485. Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
14Q LOSS MUTATED	14	127	27
14Q LOSS WILD-TYPE	114	176	194

Figure S485. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S486. Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
14Q LOSS MUTATED	10	115	96	41
14Q LOSS WILD-TYPE	109	80	201	227

Figure S486. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S487. Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
14Q LOSS MUTATED	4	39	75	106	27	11
14Q LOSS WILD-TYPE	84	106	132	53	84	158

Figure S487. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S488. Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
14Q LOSS MUTATED	40	74	145
14Q LOSS WILD-TYPE	288	118	199

Figure S488. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S489. Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
14Q LOSS MUTATED	3	235	21
14Q LOSS WILD-TYPE	74	346	185

Figure S489. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S490. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
14Q LOSS MUTATED	15	4	21	47
14Q LOSS WILD-TYPE	138	66	42	78

Figure S490. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S491. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
14Q LOSS MUTATED	5	8	22	51	1
14Q LOSS WILD-TYPE	45	81	72	81	45

Figure S491. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S492. Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
15Q LOSS MUTATED	19	5	45
15Q LOSS WILD-TYPE	263	305	245

Figure S492. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S493. Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
15Q LOSS MUTATED	4	33	9	23
15Q LOSS WILD-TYPE	115	162	288	245

Figure S493. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S494. Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
15Q LOSS MUTATED	1	27	7	24	3	7
15Q LOSS WILD-TYPE	87	118	200	135	108	162

Figure S494. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.038

Table S495. Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
15Q LOSS MUTATED	25	24	20
15Q LOSS WILD-TYPE	303	168	324

Figure S495. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.058

Table S496. Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
15Q LOSS MUTATED	1	49	19
15Q LOSS WILD-TYPE	76	532	187

Figure S496. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00413 (Fisher's exact test), Q value = 0.0064

Table S497. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
15Q LOSS MUTATED	13	2	13	8
15Q LOSS WILD-TYPE	140	68	50	117

Figure S497. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00588 (Fisher's exact test), Q value = 0.0088

Table S498. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
15Q LOSS MUTATED	3	9	16	8	0
15Q LOSS WILD-TYPE	47	80	78	124	46

Figure S498. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S499. Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
16P LOSS MUTATED	9	5	0
16P LOSS WILD-TYPE	119	298	221

Figure S499. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 4e-04

Table S500. Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
16P LOSS MUTATED	6	9	2	1
16P LOSS WILD-TYPE	113	186	295	267

Figure S500. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00281 (Fisher's exact test), Q value = 0.0044

Table S501. Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
16P LOSS MUTATED	3	7	1	6	1	0
16P LOSS WILD-TYPE	85	138	206	153	110	169

Figure S501. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.04

Table S502. Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
16P LOSS MUTATED	5	9	4
16P LOSS WILD-TYPE	323	183	340

Figure S502. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0016

Table S503. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
16P LOSS MUTATED	0	4	5	2
16P LOSS WILD-TYPE	153	66	58	123

Figure S503. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0026

Table S504. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
16P LOSS MUTATED	0	0	7	1	3
16P LOSS WILD-TYPE	50	89	87	131	43

Figure S504. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 0.00098 (Fisher's exact test), Q value = 0.0016

Table S505. Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
16Q LOSS MUTATED	7	3	18
16Q LOSS WILD-TYPE	275	307	272

Figure S505. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00884 (Fisher's exact test), Q value = 0.013

Table S506. Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
16Q LOSS MUTATED	9	10	2
16Q LOSS WILD-TYPE	119	293	219

Figure S506. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 0.0049 (Fisher's exact test), Q value = 0.0075

Table S507. Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
16Q LOSS MUTATED	7	12	5	4
16Q LOSS WILD-TYPE	112	183	292	264

Figure S507. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-04 (Fisher's exact test), Q value = 0.0012

Table S508. Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
16Q LOSS MUTATED	4	9	3	10	2	0
16Q LOSS WILD-TYPE	84	136	204	149	109	169

Figure S508. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0408 (Fisher's exact test), Q value = 0.056

Table S509. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
16Q LOSS MUTATED	2	5	5	7
16Q LOSS WILD-TYPE	151	65	58	118

Figure S509. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0137 (Fisher's exact test), Q value = 0.02

Table S510. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
16Q LOSS MUTATED	0	1	9	5	4
16Q LOSS WILD-TYPE	50	88	85	127	42

Figure S510. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0015

Table S511. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
17P LOSS MUTATED	0	5	5	2
17P LOSS WILD-TYPE	33	19	7	15

Figure S511. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0046

Table S512. Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17P LOSS MUTATED	0	5	2	0	5
17P LOSS WILD-TYPE	20	19	16	13	6

Figure S512. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S513. Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
17P LOSS MUTATED	56	6	48
17P LOSS WILD-TYPE	226	304	242

Figure S513. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S514. Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
17P LOSS MUTATED	61	18	4
17P LOSS WILD-TYPE	67	285	217

Figure S514. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S515. Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
17P LOSS MUTATED	67	27	6	10
17P LOSS WILD-TYPE	52	168	291	258

Figure S515. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S516. Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
17P LOSS MUTATED	61	16	4	26	3	0
17P LOSS WILD-TYPE	27	129	203	133	108	169

Figure S516. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S517. Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
17P LOSS MUTATED	66	22	22
17P LOSS WILD-TYPE	262	170	322

Figure S517. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S518. Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
17P LOSS MUTATED	61	46	3
17P LOSS WILD-TYPE	16	535	203

Figure S518. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S519. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
17P LOSS MUTATED	3	37	11	6
17P LOSS WILD-TYPE	150	33	52	119

Figure S519. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S520. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
17P LOSS MUTATED	0	1	12	8	36
17P LOSS WILD-TYPE	50	88	82	124	10

Figure S520. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00036

Table S521. Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
17Q LOSS MUTATED	0	4	5	0
17Q LOSS WILD-TYPE	33	20	7	17

Figure S521. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.00061

Table S522. Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
17Q LOSS MUTATED	0	4	0	0	5
17Q LOSS WILD-TYPE	20	20	18	13	6

Figure S522. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S523. Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
17Q LOSS MUTATED	53	1	28
17Q LOSS WILD-TYPE	229	309	262

Figure S523. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S524. Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
17Q LOSS MUTATED	56	7	0
17Q LOSS WILD-TYPE	72	296	221

Figure S524. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S525. Gene #72: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
17Q LOSS MUTATED	62	16	4	0
17Q LOSS WILD-TYPE	57	179	293	268

Figure S525. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S526. Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
17Q LOSS MUTATED	61	2	2	15	2	0
17Q LOSS WILD-TYPE	27	143	205	144	109	169

Figure S526. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S527. Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
17Q LOSS MUTATED	58	10	14
17Q LOSS WILD-TYPE	270	182	330

Figure S527. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S528. Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
17Q LOSS MUTATED	61	21	0
17Q LOSS WILD-TYPE	16	560	206

Figure S528. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S529. Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
17Q LOSS MUTATED	0	36	3	3
17Q LOSS WILD-TYPE	153	34	60	122

Figure S529. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S530. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
17Q LOSS MUTATED	0	0	2	4	36
17Q LOSS WILD-TYPE	50	89	92	128	10

Figure S530. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S531. Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
18P LOSS MUTATED	35	24	83
18P LOSS WILD-TYPE	247	286	207

Figure S531. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.043

Table S532. Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
18P LOSS MUTATED	22	58	24
18P LOSS WILD-TYPE	106	245	197

Figure S532. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S533. Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
18P LOSS MUTATED	13	74	17	37
18P LOSS WILD-TYPE	106	121	280	231

Figure S533. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S534. Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
18P LOSS MUTATED	11	38	16	60	6	10
18P LOSS WILD-TYPE	77	107	191	99	105	159

Figure S534. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00015

Table S535. Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
18P LOSS MUTATED	41	51	50
18P LOSS WILD-TYPE	287	141	294

Figure S535. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0048 (Fisher's exact test), Q value = 0.0073

Table S536. Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
18P LOSS MUTATED	11	111	20
18P LOSS WILD-TYPE	66	470	186

Figure S536. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0018

Table S537. Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
18P LOSS MUTATED	19	12	20	12
18P LOSS WILD-TYPE	134	58	43	113

Figure S537. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00046

Table S538. Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
18P LOSS MUTATED	1	13	27	15	7
18P LOSS WILD-TYPE	49	76	67	117	39

Figure S538. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S539. Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
18Q LOSS MUTATED	36	25	88
18Q LOSS WILD-TYPE	246	285	202

Figure S539. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 0.0465 (Fisher's exact test), Q value = 0.063

Table S540. Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
18Q LOSS MUTATED	24	59	26
18Q LOSS WILD-TYPE	104	244	195

Figure S540. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S541. Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
18Q LOSS MUTATED	15	76	17	40
18Q LOSS WILD-TYPE	104	119	280	228

Figure S541. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S542. Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
18Q LOSS MUTATED	12	44	18	59	6	9
18Q LOSS WILD-TYPE	76	101	189	100	105	160

Figure S542. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00048 (Fisher's exact test), Q value = 0.00083

Table S543. Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
18Q LOSS MUTATED	45	52	52
18Q LOSS WILD-TYPE	283	140	292

Figure S543. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00193 (Fisher's exact test), Q value = 0.0031

Table S544. Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
18Q LOSS MUTATED	12	117	20
18Q LOSS WILD-TYPE	65	464	186

Figure S544. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00071

Table S545. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
18Q LOSS MUTATED	20	13	22	13
18Q LOSS WILD-TYPE	133	57	41	112

Figure S545. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.1e-05

Table S546. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
18Q LOSS MUTATED	1	13	31	15	8
18Q LOSS WILD-TYPE	49	76	63	117	38

Figure S546. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S547. Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
19P LOSS MUTATED	10	0	17
19P LOSS WILD-TYPE	272	310	273

Figure S547. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 0.00129 (Fisher's exact test), Q value = 0.0021

Table S548. Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
19P LOSS MUTATED	3	4	16
19P LOSS WILD-TYPE	125	299	205

Figure S548. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 0.00086 (Fisher's exact test), Q value = 0.0014

Table S549. Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
19P LOSS MUTATED	1	9	2	15
19P LOSS WILD-TYPE	118	186	295	253

Figure S549. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.00058

Table S550. Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
19P LOSS MUTATED	1	13	1	6	1	5
19P LOSS WILD-TYPE	87	132	206	153	110	164

Figure S550. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.004 (Fisher's exact test), Q value = 0.0062

Table S551. Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
19P LOSS MUTATED	9	1	7	1
19P LOSS WILD-TYPE	144	69	56	124

Figure S551. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00252 (Fisher's exact test), Q value = 0.004

Table S552. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
19P LOSS MUTATED	1	4	11	1	1
19P LOSS WILD-TYPE	49	85	83	131	45

Figure S552. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00013

Table S553. Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
19Q LOSS MUTATED	8	0	14
19Q LOSS WILD-TYPE	274	310	276

Figure S553. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 0.00125 (Fisher's exact test), Q value = 0.002

Table S554. Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
19Q LOSS MUTATED	4	2	13
19Q LOSS WILD-TYPE	124	301	208

Figure S554. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.0041

Table S555. Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
19Q LOSS MUTATED	2	6	1	13
19Q LOSS WILD-TYPE	117	189	296	255

Figure S555. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.00081

Table S556. Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
19Q LOSS MUTATED	2	11	0	3	1	5
19Q LOSS WILD-TYPE	86	134	207	156	110	164

Figure S556. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 0.00464 (Fisher's exact test), Q value = 0.0071

Table S557. Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
19Q LOSS MUTATED	13	7	2
19Q LOSS WILD-TYPE	315	185	342

Figure S557. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.037

Table S558. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
19Q LOSS MUTATED	10	2	5	1
19Q LOSS WILD-TYPE	143	68	58	124

Figure S558. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.022

Table S559. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
19Q LOSS MUTATED	1	5	9	1	2
19Q LOSS WILD-TYPE	49	84	85	131	44

Figure S559. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'METHLYATION_CNMF'

P value = 0.00573 (Fisher's exact test), Q value = 0.0087

Table S560. Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
20P LOSS MUTATED	5	3	0
20P LOSS WILD-TYPE	123	300	221

Figure S560. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0034

Table S561. Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
20P LOSS MUTATED	4	6	2	0
20P LOSS WILD-TYPE	115	189	295	268

Figure S561. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.033

Table S562. Gene #77: '20p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
20P LOSS MUTATED	4	1	3	4	0	0
20P LOSS WILD-TYPE	84	144	204	155	111	169

Figure S562. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00714 (Fisher's exact test), Q value = 0.011

Table S563. Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
20P LOSS MUTATED	4	8	0
20P LOSS WILD-TYPE	73	573	206

Figure S563. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00109 (Fisher's exact test), Q value = 0.0018

Table S564. Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
20P LOSS MUTATED	0	5	0	1
20P LOSS WILD-TYPE	153	65	63	124

Figure S564. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00519 (Fisher's exact test), Q value = 0.0079

Table S565. Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
20P LOSS MUTATED	0	0	1	1	4
20P LOSS WILD-TYPE	50	89	93	131	42

Figure S565. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.00729 (Fisher's exact test), Q value = 0.011

Table S566. Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
20Q LOSS MUTATED	3	0	0
20Q LOSS WILD-TYPE	125	303	221

Figure S566. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.032

Table S567. Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
20Q LOSS MUTATED	3	2	1	0
20Q LOSS WILD-TYPE	116	193	296	268

Figure S567. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.03

Table S568. Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
20Q LOSS MUTATED	3	0	1	2	0	0
20Q LOSS WILD-TYPE	85	145	206	157	111	169

Figure S568. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.015

Table S569. Gene #78: '20q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
20Q LOSS MUTATED	3	3	0
20Q LOSS WILD-TYPE	74	578	206

Figure S569. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00811 (Fisher's exact test), Q value = 0.012

Table S570. Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
20Q LOSS MUTATED	0	3	0	0
20Q LOSS WILD-TYPE	153	67	63	125

Figure S570. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0022

Table S571. Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
20Q LOSS MUTATED	0	0	0	0	3
20Q LOSS WILD-TYPE	50	89	94	132	43

Figure S571. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.023

Table S572. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
21Q LOSS MUTATED	1	2	4	4
21Q LOSS WILD-TYPE	32	22	8	13

Figure S572. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0239 (Fisher's exact test), Q value = 0.034

Table S573. Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
21Q LOSS MUTATED	0	2	4	1	4
21Q LOSS WILD-TYPE	20	22	14	12	7

Figure S573. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S574. Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
21Q LOSS MUTATED	73	11	49
21Q LOSS WILD-TYPE	209	299	241

Figure S574. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S575. Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
21Q LOSS MUTATED	46	31	32
21Q LOSS WILD-TYPE	82	272	189

Figure S575. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S576. Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
21Q LOSS MUTATED	49	25	18	39
21Q LOSS WILD-TYPE	70	170	279	229

Figure S576. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S577. Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
21Q LOSS MUTATED	46	27	14	15	7	22
21Q LOSS WILD-TYPE	42	118	193	144	104	147

Figure S577. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S578. Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
21Q LOSS MUTATED	78	30	24
21Q LOSS WILD-TYPE	250	162	320

Figure S578. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S579. Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
21Q LOSS MUTATED	46	55	31
21Q LOSS WILD-TYPE	31	526	175

Figure S579. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S580. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
21Q LOSS MUTATED	24	27	14	11
21Q LOSS WILD-TYPE	129	43	49	114

Figure S580. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S581. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
21Q LOSS MUTATED	2	18	16	14	26
21Q LOSS WILD-TYPE	48	71	78	118	20

Figure S581. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00568 (Fisher's exact test), Q value = 0.0086

Table S582. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	33	24	12	17
22Q LOSS MUTATED	0	4	1	5
22Q LOSS WILD-TYPE	33	20	11	12

Figure S582. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.051

Table S583. Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	20	24	18	13	11
22Q LOSS MUTATED	0	4	5	0	1
22Q LOSS WILD-TYPE	20	20	13	13	10

Figure S583. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S584. Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
22Q LOSS MUTATED	41	17	49
22Q LOSS WILD-TYPE	241	293	241

Figure S584. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00046

Table S585. Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
22Q LOSS MUTATED	23	24	42
22Q LOSS WILD-TYPE	105	279	179

Figure S585. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S586. Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
22Q LOSS MUTATED	14	30	9	54
22Q LOSS WILD-TYPE	105	165	288	214

Figure S586. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S587. Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
22Q LOSS MUTATED	10	51	11	22	1	12
22Q LOSS WILD-TYPE	78	94	196	137	110	157

Figure S587. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 7.8e-05

Table S588. Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
22Q LOSS MUTATED	61	22	24
22Q LOSS WILD-TYPE	267	170	320

Figure S588. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00163 (Fisher's exact test), Q value = 0.0026

Table S589. Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
22Q LOSS MUTATED	29	14	13	7
22Q LOSS WILD-TYPE	124	56	50	118

Figure S589. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S590. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
22Q LOSS MUTATED	3	19	27	6	8
22Q LOSS WILD-TYPE	47	70	67	126	38

Figure S590. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S591. Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
XP LOSS MUTATED	63	7	48
XP LOSS WILD-TYPE	219	303	242

Figure S591. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S592. Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
XP LOSS MUTATED	53	28	15
XP LOSS WILD-TYPE	75	275	206

Figure S592. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S593. Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
XP LOSS MUTATED	54	18	20	26
XP LOSS WILD-TYPE	65	177	277	242

Figure S593. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S594. Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
XP LOSS MUTATED	49	30	13	14	7	5
XP LOSS WILD-TYPE	39	115	194	145	104	164

Figure S594. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S595. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
XP LOSS MUTATED	73	18	26
XP LOSS WILD-TYPE	255	174	318

Figure S595. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S596. Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
XP LOSS MUTATED	48	55	14
XP LOSS WILD-TYPE	29	526	192

Figure S596. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S597. Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
XP LOSS MUTATED	10	34	10	9
XP LOSS WILD-TYPE	143	36	53	116

Figure S597. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S598. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
XP LOSS MUTATED	2	5	19	8	29
XP LOSS WILD-TYPE	48	84	75	124	17

Figure S598. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S599. Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	282	310	290
XQ LOSS MUTATED	62	4	50
XQ LOSS WILD-TYPE	220	306	240

Figure S599. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S600. Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	128	303	221
XQ LOSS MUTATED	53	25	15
XQ LOSS WILD-TYPE	75	278	206

Figure S600. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S601. Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	119	195	297	268
XQ LOSS MUTATED	52	20	18	26
XQ LOSS WILD-TYPE	67	175	279	242

Figure S601. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S602. Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	88	145	207	159	111	169
XQ LOSS MUTATED	47	32	12	14	6	5
XQ LOSS WILD-TYPE	41	113	195	145	105	164

Figure S602. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S603. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	328	192	344
XQ LOSS MUTATED	70	18	27
XQ LOSS WILD-TYPE	258	174	317

Figure S603. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S604. Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	77	581	206
XQ LOSS MUTATED	46	56	13
XQ LOSS WILD-TYPE	31	525	193

Figure S604. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S605. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	153	70	63	125
XQ LOSS MUTATED	10	33	11	8
XQ LOSS WILD-TYPE	143	37	52	117

Figure S605. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.1e-05

Table S606. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	50	89	94	132	46
XQ LOSS MUTATED	2	5	21	6	28
XQ LOSS WILD-TYPE	48	84	73	126	18

Figure S606. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/15087102/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/15165233/KIPAN-TP.transferedmergedcluster.txt
Number of patients = 882
Number of significantly arm-level cnvs = 82
Number of molecular subtypes = 10
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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