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

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 12 molecular subtypes across 539 patients, 696 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 696 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
4p loss	106 (20%)	433	0.00366 (0.00655)	0.00181 (0.00342)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)
4q loss	104 (19%)	435	0.0426 (0.0615)	0.00793 (0.0134)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)
5p loss	53 (10%)	486	0.0429 (0.0617)	0.0402 (0.0585)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00035 (0.000733)	9e-05 (0.000208)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	5e-05 (0.00012)	0.00022 (0.00048)
5q loss	73 (14%)	466	0.0114 (0.0185)	0.0101 (0.0165)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)
8p loss	78 (14%)	461	0.00872 (0.0145)	4e-05 (9.77e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)
9p loss	99 (18%)	440	0.00126 (0.00244)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	9e-05 (0.000208)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00384 (0.00686)	0.0184 (0.0289)
9q loss	117 (22%)	422	5e-05 (0.00012)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00012 (0.000272)	0.0013 (0.0025)
14q loss	62 (12%)	477	0.00252 (0.00467)	0.00055 (0.00112)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0013 (0.0025)	5e-05 (0.00012)
15q loss	109 (20%)	430	0.00049 (0.00101)	4e-05 (9.77e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)
16p loss	99 (18%)	440	0.00232 (0.00434)	0.00785 (0.0132)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00014 (0.000314)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0003 (0.000638)	1e-05 (2.82e-05)
16q loss	140 (26%)	399	0.00088 (0.00176)	0.00143 (0.00272)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00028 (0.000603)	1e-05 (2.82e-05)
17p loss	129 (24%)	410	0.00319 (0.00577)	0.00017 (0.000376)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	0.00027 (0.000584)
17q loss	93 (17%)	446	0.00248 (0.00461)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00552 (0.0096)	0.0221 (0.0344)
21q loss	54 (10%)	485	0.0363 (0.0534)	0.029 (0.0444)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0171 (0.027)	0.00127 (0.00245)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	2e-05 (5.26e-05)
22q loss	110 (20%)	429	0.00261 (0.00481)	0.00711 (0.0121)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00969 (0.0159)	0.00122 (0.00237)
xp loss	86 (16%)	453	0.00059 (0.0012)	0.0009 (0.0018)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	3e-05 (7.55e-05)	3e-05 (7.55e-05)
xq loss	70 (13%)	469	0.00247 (0.0046)	0.00752 (0.0128)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00287 (0.00523)	1e-05 (2.82e-05)
8q gain	159 (29%)	380	0.0166 (0.0263)	0.0303 (0.046)	1e-05 (2.82e-05)	0.206 (0.258)	0.0155 (0.0246)	3e-05 (7.55e-05)	3e-05 (7.55e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00832 (0.0139)	0.00257 (0.00474)	0.00764 (0.013)
19p gain	55 (10%)	484	0.0362 (0.0534)	0.0291 (0.0445)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00279 (0.0051)	3e-05 (7.55e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	5e-05 (0.00012)	0.104 (0.14)
20p gain	109 (20%)	430	0.0353 (0.0524)	0.194 (0.245)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	5e-05 (0.00012)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00159 (0.00301)	0.00011 (0.000251)
20q gain	130 (24%)	409	0.00829 (0.0139)	0.0505 (0.0711)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	0.0001 (0.000229)
3p loss	52 (10%)	487	0.0365 (0.0536)	0.00071 (0.00143)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0006 (0.00122)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0645 (0.0895)	9e-05 (0.000208)
3q loss	31 (6%)	508	0.0361 (0.0533)	0.00068 (0.00138)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	0.0342 (0.0511)	0.0005 (0.00103)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00075 (0.00151)	0.00016 (0.000356)	0.288 (0.351)	0.0468 (0.0665)
10p loss	44 (8%)	495	0.0358 (0.053)	0.0302 (0.0459)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	9e-05 (0.000208)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0691 (0.0956)	0.00087 (0.00174)
2p gain	93 (17%)	446	0.524 (0.599)	0.37 (0.44)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00426 (0.00754)	0.0248 (0.0383)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00019 (0.000419)	5e-05 (0.00012)
2q gain	78 (14%)	461	0.465 (0.54)	0.947 (1.00)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0025 (0.00464)	0.00827 (0.0139)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0001 (0.000229)	3e-05 (7.55e-05)
3q gain	85 (16%)	454	0.624 (0.699)	0.25 (0.309)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00765 (0.013)	0.00111 (0.00217)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00087 (0.00174)	3e-05 (7.55e-05)
5p gain	52 (10%)	487	1 (1.00)	0.515 (0.59)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0125 (0.02)	0.0003 (0.000638)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00132 (0.00253)	2e-05 (5.26e-05)
6p gain	81 (15%)	458	0.689 (0.762)	0.738 (0.811)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	0.00782 (0.0132)	0.00015 (0.000335)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	1e-05 (2.82e-05)	0.00091 (0.00181)	0.0121 (0.0194)
13q gain	30 (6%)	509	0.133 (0.175)	0.0064 (0.011)	1e-05 (2.82e-05)	8e-05 (0.000187)	0.0604 (0.0841)	0.00263 (0.00484)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	0.028 (0.0431)	0.01 (0.0165)
18p gain	73 (14%)	466	0.411 (0.484)	0.238 (0.296)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00013 (0.000293)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	1e-05 (2.82e-05)
18q gain	46 (9%)	493	0.109 (0.146)	0.18 (0.23)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	8e-05 (0.000187)	0.0119 (0.0192)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00546 (0.00951)	1e-05 (2.82e-05)
19q gain	58 (11%)	481	0.134 (0.175)	0.166 (0.214)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	0.00306 (0.00556)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00016 (0.000356)	0.0199 (0.0313)
21q gain	39 (7%)	500			1e-05 (2.82e-05)	0.0001 (0.000229)	0.00017 (0.000376)	0.0003 (0.000638)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00414 (0.00734)	0.0446 (0.0638)
22q gain	30 (6%)	509			1e-05 (2.82e-05)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00014 (0.000314)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	6e-05 (0.000142)
6q loss	25 (5%)	514	0.348 (0.419)	0.0294 (0.045)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0464 (0.0661)	0.108 (0.145)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00033 (0.000692)	1e-05 (2.82e-05)	0.00881 (0.0146)	0.0138 (0.022)
7q loss	45 (8%)	494			1e-05 (2.82e-05)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	0.00093 (0.00184)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	6e-05 (0.000142)	0.00305 (0.00555)
8q loss	22 (4%)	517			1e-05 (2.82e-05)	2e-05 (5.26e-05)	0.00277 (0.00508)	0.00051 (0.00105)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	3e-05 (7.55e-05)	0.00126 (0.00244)
10q loss	40 (7%)	499	0.134 (0.175)	0.166 (0.214)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00655 (0.0113)	3e-05 (7.55e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00392 (0.00696)	0.0125 (0.02)
11p loss	76 (14%)	463			1e-05 (2.82e-05)	1e-05 (2.82e-05)	6e-05 (0.000142)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00011 (0.000251)	0.0002 (0.000439)
11q loss	73 (14%)	466			1e-05 (2.82e-05)	1e-05 (2.82e-05)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)
12p loss	45 (8%)	494	0.135 (0.176)	0.168 (0.216)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	0.00027 (0.000584)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00337 (0.00606)	0.00589 (0.0102)
12q loss	40 (7%)	499			1e-05 (2.82e-05)	5e-05 (0.00012)	0.0005 (0.00103)	3e-05 (7.55e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0014 (0.00267)	0.00031 (0.000655)
13q loss	93 (17%)	446	1 (1.00)	0.194 (0.245)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	7e-05 (0.000165)	0.00149 (0.00282)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0414 (0.0599)	0.0237 (0.0369)
18p loss	51 (9%)	488			1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0271 (0.0418)	0.00101 (0.00198)	2e-05 (5.26e-05)	2e-05 (5.26e-05)	3e-05 (7.55e-05)	0.00319 (0.00577)	0.00897 (0.0149)	0.0109 (0.0177)
18q loss	63 (12%)	476			1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0101 (0.0165)	0.00099 (0.00195)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	3e-05 (7.55e-05)	0.0114 (0.0185)	0.0113 (0.0183)
19p loss	57 (11%)	482			1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00013 (0.000293)	0.00012 (0.000272)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00385 (0.00686)	1e-05 (2.82e-05)
19q loss	54 (10%)	485	0.759 (0.831)	0.056 (0.0784)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	3e-05 (7.55e-05)	9e-05 (0.000208)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	4e-05 (9.77e-05)	0.00601 (0.0104)	0.00037 (0.000773)
12p gain	69 (13%)	470	0.579 (0.654)	0.688 (0.761)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.291 (0.353)	0.0492 (0.0695)	2e-05 (5.26e-05)	4e-05 (9.77e-05)	0.00136 (0.0026)	1e-05 (2.82e-05)	0.00676 (0.0116)	0.00092 (0.00183)
1p loss	27 (5%)	512			1e-05 (2.82e-05)	3e-05 (7.55e-05)	0.0481 (0.0682)	0.00014 (0.000314)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00044 (0.00091)	1e-05 (2.82e-05)	0.224 (0.279)	0.0413 (0.0599)
6p loss	20 (4%)	519	0.352 (0.422)	0.0299 (0.0456)	1e-05 (2.82e-05)	0.00033 (0.000692)	0.0377 (0.0552)	0.0563 (0.0785)	0.00011 (0.000251)	0.0003 (0.000638)	0.00352 (0.00631)	0.0004 (0.000829)	0.0102 (0.0167)	0.0799 (0.109)
7p loss	45 (8%)	494	0.0363 (0.0534)	0.194 (0.245)	1e-05 (2.82e-05)	3e-05 (7.55e-05)	0.00202 (0.00379)	0.0039 (0.00694)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.0552 (0.0774)	0.0538 (0.0755)
1p gain	54 (10%)	485	0.316 (0.382)	0.261 (0.321)	1e-05 (2.82e-05)	0.0184 (0.0289)	0.471 (0.546)	0.456 (0.53)	6e-05 (0.000142)	0.00029 (0.000622)	1e-05 (2.82e-05)	0.00021 (0.000459)	0.00326 (0.00588)	0.0395 (0.0577)
1q gain	189 (35%)	350	0.267 (0.327)	0.00928 (0.0153)	1e-05 (2.82e-05)	0.108 (0.144)	0.00021 (0.000459)	0.00094 (0.00185)	0.0116 (0.0187)	0.00028 (0.000603)	0.00017 (0.000376)	0.184 (0.234)	0.318 (0.383)	0.0144 (0.023)
9p gain	22 (4%)	517			0.00063 (0.00128)	0.0366 (0.0537)	0.00029 (0.000622)	0.00476 (0.00835)	0.00454 (0.00799)	0.0281 (0.0433)	0.00246 (0.00459)	0.0208 (0.0326)	0.506 (0.581)	0.296 (0.359)
17q gain	30 (6%)	509			1e-05 (2.82e-05)	1e-05 (2.82e-05)	0.00031 (0.000655)	0.326 (0.393)	2e-05 (5.26e-05)	1e-05 (2.82e-05)	6e-05 (0.000142)	1e-05 (2.82e-05)	0.0945 (0.127)	0.0344 (0.0512)
5q gain	20 (4%)	519			3e-05 (7.55e-05)	0.0147 (0.0234)	0.649 (0.724)	0.074 (0.102)	0.00213 (0.00399)	0.00663 (0.0114)	0.00444 (0.00784)	0.00093 (0.00184)	0.0562 (0.0785)	0.0004 (0.000829)
6q gain	66 (12%)	473	0.687 (0.761)	0.74 (0.812)	1e-05 (2.82e-05)	0.00052 (0.00106)	0.0836 (0.113)	0.0004 (0.000829)	6e-05 (0.000142)	0.0004 (0.000829)	0.0082 (0.0138)	0.00109 (0.00213)	0.247 (0.306)	0.19 (0.241)
11p gain	23 (4%)	516	0.0358 (0.053)	0.195 (0.245)	2e-05 (5.26e-05)	0.0392 (0.0573)	0.122 (0.162)	0.254 (0.314)	0.0002 (0.000439)	0.00138 (0.00264)	0.0146 (0.0232)	0.0117 (0.0189)	0.384 (0.456)	0.262 (0.321)
1q loss	16 (3%)	523			2e-05 (5.26e-05)	0.00635 (0.011)	0.365 (0.436)	0.0244 (0.0379)	0.00092 (0.00183)	0.00108 (0.00212)	0.0288 (0.0443)	0.00026 (0.000566)	0.799 (0.871)	0.246 (0.305)
3p gain	48 (9%)	491			1e-05 (2.82e-05)	0.00284 (0.00518)	0.615 (0.69)	0.132 (0.174)	3e-05 (7.55e-05)	0.00709 (0.0121)	0.0215 (0.0335)	0.0297 (0.0452)	0.258 (0.318)	0.154 (0.2)
14q gain	36 (7%)	503	1 (1.00)	0.842 (0.912)	1e-05 (2.82e-05)	0.0305 (0.0462)	0.188 (0.239)	0.2 (0.252)	1e-05 (2.82e-05)	0.0012 (0.00234)	0.00027 (0.000584)	0.00343 (0.00616)	0.362 (0.433)	0.309 (0.374)
16p gain	25 (5%)	514			1e-05 (2.82e-05)	0.00325 (0.00587)	0.0766 (0.105)	0.0821 (0.111)	0.00927 (0.0153)	0.049 (0.0694)	0.0209 (0.0326)	0.0478 (0.0678)	0.179 (0.228)	0.659 (0.734)
2q loss	18 (3%)	521			1e-05 (2.82e-05)	0.0411 (0.0598)	0.411 (0.484)	0.222 (0.277)	2e-05 (5.26e-05)	0.0072 (0.0123)	0.00873 (0.0145)	0.0426 (0.0615)	0.513 (0.588)	0.471 (0.546)
4p gain	14 (3%)	525			5e-05 (0.00012)	0.485 (0.561)	0.433 (0.507)	0.0322 (0.0487)	0.00142 (0.0027)	0.0435 (0.0625)	0.0732 (0.101)	0.0118 (0.019)	0.501 (0.577)	0.299 (0.363)
7p gain	68 (13%)	471	0.897 (0.962)	0.906 (0.971)	1e-05 (2.82e-05)	0.0051 (0.00891)	0.553 (0.629)	0.0503 (0.0711)	0.00865 (0.0144)	0.0505 (0.0711)	0.0314 (0.0475)	0.197 (0.249)	0.00032 (0.000674)	0.33 (0.397)
17p gain	13 (2%)	526			0.0385 (0.0563)	0.17 (0.217)	0.189 (0.239)	0.477 (0.552)	0.0084 (0.014)	0.017 (0.0269)	0.221 (0.276)	0.00461 (0.0081)	0.0341 (0.051)	0.716 (0.788)
20p loss	22 (4%)	517	0.849 (0.919)	0.165 (0.214)	1e-05 (2.82e-05)	0.141 (0.184)	0.154 (0.199)	0.0432 (0.0621)	0.0242 (0.0376)	0.0117 (0.0189)	0.0814 (0.111)	0.0102 (0.0167)	0.265 (0.325)	0.375 (0.446)
8p gain	116 (22%)	423	0.434 (0.508)	0.406 (0.479)	1e-05 (2.82e-05)	0.618 (0.692)	0.626 (0.7)	0.00276 (0.00507)	0.0467 (0.0665)	0.0517 (0.0727)	0.0344 (0.0512)	0.426 (0.501)	0.08 (0.109)	0.113 (0.15)
10p gain	116 (22%)	423	0.00499 (0.00874)	0.0881 (0.119)	0.0338 (0.0508)	0.571 (0.646)	0.0346 (0.0514)	0.553 (0.629)	0.218 (0.272)	0.117 (0.155)	0.146 (0.189)	0.224 (0.279)	0.0338 (0.0508)	0.0866 (0.117)
12q gain	51 (9%)	488	0.579 (0.654)	0.686 (0.761)	1e-05 (2.82e-05)	0.00121 (0.00235)	0.752 (0.824)	0.585 (0.66)	0.0337 (0.0507)	0.0782 (0.107)	0.26 (0.319)	0.0163 (0.0258)	0.364 (0.435)	0.0818 (0.111)
20q loss	11 (2%)	528			0.00187 (0.00353)	0.0162 (0.0257)	0.034 (0.0509)	0.186 (0.237)	0.0734 (0.101)	0.0638 (0.0887)	0.189 (0.239)	0.00545 (0.00951)	0.487 (0.562)	0.117 (0.156)
7q gain	65 (12%)	474	0.94 (1.00)	1 (1.00)	1e-05 (2.82e-05)	0.0592 (0.0826)	0.891 (0.957)	0.129 (0.17)	0.0813 (0.111)	0.034 (0.0509)	0.131 (0.173)	0.432 (0.507)	0.00735 (0.0125)	0.851 (0.92)
11q gain	20 (4%)	519	0.134 (0.175)	0.166 (0.214)	9e-05 (0.000208)	0.0254 (0.0393)	0.161 (0.208)	0.444 (0.518)	0.00189 (0.00356)	0.0647 (0.0897)	0.258 (0.318)	0.107 (0.144)	0.965 (1.00)	0.693 (0.765)
2p loss	12 (2%)	527			0.00031 (0.000655)	0.0884 (0.119)	0.289 (0.352)	0.424 (0.498)	0.0007 (0.00141)	0.0415 (0.06)	0.076 (0.104)	0.204 (0.256)	0.565 (0.641)	0.546 (0.623)
9q gain	10 (2%)	529			0.0935 (0.126)	0.367 (0.438)	0.593 (0.667)	0.0433 (0.0622)	0.391 (0.463)	0.372 (0.443)	0.0335 (0.0505)	0.394 (0.467)	0.837 (0.909)	0.331 (0.398)
xp gain	63 (12%)	476	0.861 (0.928)	0.926 (0.99)	1e-05 (2.82e-05)	0.675 (0.751)	0.876 (0.943)	0.774 (0.846)	0.551 (0.628)	0.803 (0.874)	0.704 (0.776)	0.913 (0.977)	0.0458 (0.0654)	0.41 (0.484)
xq gain	64 (12%)	475	0.731 (0.804)	0.478 (0.552)	1e-05 (2.82e-05)	1 (1.00)	0.696 (0.768)	0.456 (0.53)	0.388 (0.46)	0.933 (0.996)	0.588 (0.663)	0.97 (1.00)	0.00452 (0.00797)	0.853 (0.921)
4q gain	8 (1%)	531			0.00599 (0.0104)	0.861 (0.928)	0.57 (0.646)	0.146 (0.189)	0.175 (0.224)	0.442 (0.516)	0.565 (0.641)	0.281 (0.343)	0.268 (0.327)	0.673 (0.749)
10q gain	108 (20%)	431	0.00257 (0.00474)	0.0887 (0.12)	0.14 (0.183)	0.452 (0.527)	0.114 (0.152)	0.506 (0.581)	0.137 (0.179)	0.358 (0.429)	0.169 (0.217)	0.128 (0.169)	0.0779 (0.107)	0.0713 (0.0986)
15q gain	11 (2%)	528			0.00898 (0.0149)	0.764 (0.835)	0.0977 (0.131)	0.257 (0.317)	0.883 (0.949)	0.59 (0.664)	0.798 (0.871)	0.686 (0.761)	0.497 (0.573)	0.838 (0.909)
16q gain	10 (2%)	529			0.0438 (0.0627)	0.601 (0.675)	0.215 (0.27)	0.24 (0.298)	0.142 (0.185)	0.632 (0.706)	0.831 (0.904)	0.524 (0.599)	1 (1.00)	1 (1.00)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
1P GAIN MUTATED	39	4	4	7
1P GAIN WILD-TYPE	169	174	95	47

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.029

Table S2. Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
1P GAIN MUTATED	25	7	13
1P GAIN WILD-TYPE	129	71	180

Figure S2. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S3. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
1P GAIN MUTATED	35	6	7	6
1P GAIN WILD-TYPE	153	117	86	127

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.00062

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
1P GAIN MUTATED	26	2	7	4	9	4	2
1P GAIN WILD-TYPE	97	51	40	61	99	62	73

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S5. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
1P GAIN MUTATED	33	7	9	3	1
1P GAIN WILD-TYPE	131	73	97	130	46

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00046

Table S6. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
1P GAIN MUTATED	15	31	7
1P GAIN WILD-TYPE	203	141	133

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00326 (Fisher's exact test), Q value = 0.0059

Table S7. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
1P GAIN MUTATED	23	5	6	11
1P GAIN WILD-TYPE	93	93	86	81

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0395 (Fisher's exact test), Q value = 0.058

Table S8. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
1P GAIN MUTATED	25	8	12
1P GAIN WILD-TYPE	138	124	91

Figure S8. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00928 (Fisher's exact test), Q value = 0.015

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
1Q GAIN MUTATED	7	2	6	5	3
1Q GAIN WILD-TYPE	7	7	1	2	13

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S10. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
1Q GAIN MUTATED	77	24	37	51
1Q GAIN WILD-TYPE	131	154	62	3

Figure S10. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'RPPA_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00046

Table S11. Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
1Q GAIN MUTATED	20	40	11	24	18	20	21
1Q GAIN WILD-TYPE	19	41	41	32	66	48	32

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00094 (Fisher's exact test), Q value = 0.0019

Table S12. Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
1Q GAIN MUTATED	56	55	29	14
1Q GAIN WILD-TYPE	52	127	64	36

Figure S12. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q gain' versus 'MRNASEQ_CNMF'

P value = 0.0116 (Fisher's exact test), Q value = 0.019

Table S13. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
1Q GAIN MUTATED	69	52	36	32
1Q GAIN WILD-TYPE	119	71	57	101

Figure S13. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 6e-04

Table S14. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
1Q GAIN MUTATED	49	28	11	33	33	17	18
1Q GAIN WILD-TYPE	74	25	36	32	75	49	57

Figure S14. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q gain' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00038

Table S15. Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
1Q GAIN MUTATED	64	44	35	34	11
1Q GAIN WILD-TYPE	100	36	71	99	36

Figure S15. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.023

Table S16. Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
1Q GAIN MUTATED	61	33	43
1Q GAIN WILD-TYPE	102	99	60

Figure S16. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
2P GAIN MUTATED	68	2	17	6
2P GAIN WILD-TYPE	140	176	82	48

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S18. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
2P GAIN MUTATED	43	17	12
2P GAIN WILD-TYPE	111	61	181

Figure S18. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.0075

Table S19. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
2P GAIN MUTATED	4	4	7	13	20	14	13
2P GAIN WILD-TYPE	35	77	45	43	64	54	40

Figure S19. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.038

Table S20. Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
2P GAIN MUTATED	10	42	15	8
2P GAIN WILD-TYPE	98	140	78	42

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S21. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
2P GAIN MUTATED	58	13	13	9
2P GAIN WILD-TYPE	130	110	80	124

Figure S21. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S22. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
2P GAIN MUTATED	48	7	10	4	14	6	4
2P GAIN WILD-TYPE	75	46	37	61	94	60	71

Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S23. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
2P GAIN MUTATED	52	9	14	8	9
2P GAIN WILD-TYPE	112	71	92	125	38

Figure S23. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S24. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
2P GAIN MUTATED	25	57	10
2P GAIN WILD-TYPE	193	115	130

Figure S24. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00042

Table S25. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
2P GAIN MUTATED	33	6	17	13
2P GAIN WILD-TYPE	83	92	75	79

Figure S25. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S26. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
2P GAIN MUTATED	36	8	25
2P GAIN WILD-TYPE	127	124	78

Figure S26. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S27. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
2Q GAIN MUTATED	56	1	16	5
2Q GAIN WILD-TYPE	152	177	83	49

Figure S27. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S28. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
2Q GAIN MUTATED	39	14	11
2Q GAIN WILD-TYPE	115	64	182

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

'2q gain' versus 'RPPA_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.0046

Table S29. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
2Q GAIN MUTATED	3	3	7	12	19	12	12
2Q GAIN WILD-TYPE	36	78	45	44	65	56	41

Figure S29. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00827 (Fisher's exact test), Q value = 0.014

Table S30. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
2Q GAIN MUTATED	7	38	16	7
2Q GAIN WILD-TYPE	101	144	77	43

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S31. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
2Q GAIN MUTATED	50	10	11	7
2Q GAIN WILD-TYPE	138	113	82	126

Figure S31. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S32. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
2Q GAIN MUTATED	41	5	8	3	12	5	4
2Q GAIN WILD-TYPE	82	48	39	62	96	61	71

Figure S32. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S33. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
2Q GAIN MUTATED	47	7	11	6	7
2Q GAIN WILD-TYPE	117	73	95	127	40

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S34. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
2Q GAIN MUTATED	21	49	8
2Q GAIN WILD-TYPE	197	123	132

Figure S34. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S35. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
2Q GAIN MUTATED	32	5	13	12
2Q GAIN WILD-TYPE	84	93	79	80

Figure S35. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S36. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
2Q GAIN MUTATED	34	6	22
2Q GAIN WILD-TYPE	129	126	81

Figure S36. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S37. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
3P GAIN MUTATED	39	0	8	1
3P GAIN WILD-TYPE	169	178	91	53

Figure S37. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00284 (Fisher's exact test), Q value = 0.0052

Table S38. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
3P GAIN MUTATED	25	7	10
3P GAIN WILD-TYPE	129	71	183

Figure S38. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S39. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
3P GAIN MUTATED	32	2	6	8
3P GAIN WILD-TYPE	156	121	87	125

Figure S39. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00709 (Fisher's exact test), Q value = 0.012

Table S40. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
3P GAIN MUTATED	16	0	8	4	13	3	4
3P GAIN WILD-TYPE	107	53	39	61	95	63	71

Figure S40. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.0215 (Fisher's exact test), Q value = 0.034

Table S41. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
3P GAIN MUTATED	25	4	6	8	5
3P GAIN WILD-TYPE	139	76	100	125	42

Figure S41. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.045

Table S42. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
3P GAIN MUTATED	14	24	10
3P GAIN WILD-TYPE	204	148	130

Figure S42. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S43. Gene #6: '3q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
3Q GAIN MUTATED	74	0	10	1
3Q GAIN WILD-TYPE	134	178	89	53

Figure S43. 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 = 2.8e-05

Table S44. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
3Q GAIN MUTATED	48	16	11
3Q GAIN WILD-TYPE	106	62	182

Figure S44. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 0.00765 (Fisher's exact test), Q value = 0.013

Table S45. Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
3Q GAIN MUTATED	3	5	4	16	14	12	6
3Q GAIN WILD-TYPE	36	76	48	40	70	56	47

Figure S45. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.0022

Table S46. Gene #6: '3q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
3Q GAIN MUTATED	5	36	15	4
3Q GAIN WILD-TYPE	103	146	78	46

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S47. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
3Q GAIN MUTATED	60	2	14	9
3Q GAIN WILD-TYPE	128	121	79	124

Figure S47. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S48. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
3Q GAIN MUTATED	38	0	18	4	17	3	5
3Q GAIN WILD-TYPE	85	53	29	61	91	63	70

Figure S48. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S49. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
3Q GAIN MUTATED	50	4	13	9	9
3Q GAIN WILD-TYPE	114	76	93	124	38

Figure S49. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S50. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
3Q GAIN MUTATED	17	57	11
3Q GAIN WILD-TYPE	201	115	129

Figure S50. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00087 (Fisher's exact test), Q value = 0.0017

Table S51. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
3Q GAIN MUTATED	29	6	15	21
3Q GAIN WILD-TYPE	87	92	77	71

Figure S51. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S52. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
3Q GAIN MUTATED	42	9	20
3Q GAIN WILD-TYPE	121	123	83

Figure S52. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S53. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
4P GAIN MUTATED	14	0	0	0
4P GAIN WILD-TYPE	194	178	99	54

Figure S53. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0322 (Fisher's exact test), Q value = 0.049

Table S54. Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
4P GAIN MUTATED	0	9	4	0
4P GAIN WILD-TYPE	108	173	89	50

Figure S54. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0027

Table S55. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
4P GAIN MUTATED	12	1	0	1
4P GAIN WILD-TYPE	176	122	93	132

Figure S55. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0435 (Fisher's exact test), Q value = 0.062

Table S56. Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
4P GAIN MUTATED	8	0	2	0	3	1	0
4P GAIN WILD-TYPE	115	53	45	65	105	65	75

Figure S56. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.019

Table S57. Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
4P GAIN MUTATED	3	10	1
4P GAIN WILD-TYPE	215	162	139

Figure S57. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.01

Table S58. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
4Q GAIN MUTATED	8	0	0	0
4Q GAIN WILD-TYPE	200	178	99	54

Figure S58. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S59. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
5P GAIN MUTATED	47	0	3	2
5P GAIN WILD-TYPE	161	178	96	52

Figure S59. 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 = 2.8e-05

Table S60. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
5P GAIN MUTATED	31	8	6
5P GAIN WILD-TYPE	123	70	187

Figure S60. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'RPPA_CNMF'

P value = 0.0125 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
5P GAIN MUTATED	1	5	3	11	16	5	5
5P GAIN WILD-TYPE	38	76	49	45	68	63	48

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

'5p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S62. Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
5P GAIN MUTATED	5	33	7	1
5P GAIN WILD-TYPE	103	149	86	49

Figure S62. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S63. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
5P GAIN MUTATED	40	6	6	0
5P GAIN WILD-TYPE	148	117	87	133

Figure S63. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S64. Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
5P GAIN MUTATED	28	3	12	1	6	2	0
5P GAIN WILD-TYPE	95	50	35	64	102	64	75

Figure S64. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
5P GAIN MUTATED	37	5	6	1	3
5P GAIN WILD-TYPE	127	75	100	132	44

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

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S66. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
5P GAIN MUTATED	13	38	1
5P GAIN WILD-TYPE	205	134	139

Figure S66. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00132 (Fisher's exact test), Q value = 0.0025

Table S67. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
5P GAIN MUTATED	20	2	9	12
5P GAIN WILD-TYPE	96	96	83	80

Figure S67. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S68. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
5P GAIN MUTATED	29	3	11
5P GAIN WILD-TYPE	134	129	92

Figure S68. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S69. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
5Q GAIN MUTATED	18	0	1	1
5Q GAIN WILD-TYPE	190	178	98	53

Figure S69. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.023

Table S70. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
5Q GAIN MUTATED	13	2	4
5Q GAIN WILD-TYPE	141	76	189

Figure S70. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00213 (Fisher's exact test), Q value = 0.004

Table S71. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
5Q GAIN MUTATED	14	3	3	0
5Q GAIN WILD-TYPE	174	120	90	133

Figure S71. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00663 (Fisher's exact test), Q value = 0.011

Table S72. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
5Q GAIN MUTATED	7	2	6	1	4	0	0
5Q GAIN WILD-TYPE	116	51	41	64	104	66	75

Figure S72. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.0078

Table S73. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
5Q GAIN MUTATED	12	4	2	0	2
5Q GAIN WILD-TYPE	152	76	104	133	45

Figure S73. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0018

Table S74. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
5Q GAIN MUTATED	7	13	0
5Q GAIN WILD-TYPE	211	159	140

Figure S74. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

Table S75. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
5Q GAIN MUTATED	14	0	3
5Q GAIN WILD-TYPE	149	132	100

Figure S75. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
6P GAIN MUTATED	72	2	5	2
6P GAIN WILD-TYPE	136	176	94	52

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

'6p gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
6P GAIN MUTATED	42	15	14
6P GAIN WILD-TYPE	112	63	179

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

'6p gain' versus 'RPPA_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.013

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
6P GAIN MUTATED	2	6	4	13	20	10	9
6P GAIN WILD-TYPE	37	75	48	43	64	58	44

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

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00034

Table S79. Gene #11: '6p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
6P GAIN MUTATED	4	40	15	5
6P GAIN WILD-TYPE	104	142	78	45

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

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S80. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
6P GAIN MUTATED	54	6	6	15
6P GAIN WILD-TYPE	134	117	87	118

Figure S80. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S81. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
6P GAIN MUTATED	42	0	6	5	14	8	6
6P GAIN WILD-TYPE	81	53	41	60	94	58	69

Figure S81. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S82. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
6P GAIN MUTATED	45	6	10	12	8
6P GAIN WILD-TYPE	119	74	96	121	39

Figure S82. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S83. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
6P GAIN MUTATED	21	48	12
6P GAIN WILD-TYPE	197	124	128

Figure S83. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0018

Table S84. Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
6P GAIN MUTATED	34	10	11	13
6P GAIN WILD-TYPE	82	88	81	79

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.019

Table S85. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
6P GAIN MUTATED	37	13	18
6P GAIN WILD-TYPE	126	119	85

Figure S85. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S86. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
6Q GAIN MUTATED	59	1	5	1
6Q GAIN WILD-TYPE	149	177	94	53

Figure S86. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0011

Table S87. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
6Q GAIN MUTATED	33	10	14
6Q GAIN WILD-TYPE	121	68	179

Figure S87. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
6Q GAIN MUTATED	3	33	12	4
6Q GAIN WILD-TYPE	105	149	81	46

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

'6q gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S89. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
6Q GAIN MUTATED	40	6	6	14
6Q GAIN WILD-TYPE	148	117	87	119

Figure S89. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

Table S90. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
6Q GAIN MUTATED	28	0	7	5	12	8	6
6Q GAIN WILD-TYPE	95	53	40	60	96	58	69

Figure S90. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.0082 (Fisher's exact test), Q value = 0.014

Table S91. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
6Q GAIN MUTATED	33	6	9	11	7
6Q GAIN WILD-TYPE	131	74	97	122	40

Figure S91. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.0021

Table S92. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
6Q GAIN MUTATED	20	35	11
6Q GAIN WILD-TYPE	198	137	129

Figure S92. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S93. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
7P GAIN MUTATED	43	2	15	8
7P GAIN WILD-TYPE	165	176	84	46

Figure S93. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.0051 (Fisher's exact test), Q value = 0.0089

Table S94. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
7P GAIN MUTATED	29	4	19
7P GAIN WILD-TYPE	125	74	174

Figure S94. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.014

Table S95. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
7P GAIN MUTATED	36	14	6	12
7P GAIN WILD-TYPE	152	109	87	121

Figure S95. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.048

Table S96. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
7P GAIN MUTATED	30	13	9	10	5
7P GAIN WILD-TYPE	134	67	97	123	42

Figure S96. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00067

Table S97. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
7P GAIN MUTATED	26	4	12	7
7P GAIN WILD-TYPE	90	94	80	85

Figure S97. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S98. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
7Q GAIN MUTATED	37	4	15	9
7Q GAIN WILD-TYPE	171	174	84	45

Figure S98. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.051

Table S99. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
7Q GAIN MUTATED	19	8	8	1	15	8	6
7Q GAIN WILD-TYPE	104	45	39	64	93	58	69

Figure S99. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.013

Table S100. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
7Q GAIN MUTATED	22	5	13	7
7Q GAIN WILD-TYPE	94	93	79	85

Figure S100. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S101. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
8P GAIN MUTATED	64	7	40	5
8P GAIN WILD-TYPE	144	171	59	49

Figure S101. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00276 (Fisher's exact test), Q value = 0.0051

Table S102. Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
8P GAIN MUTATED	14	33	31	13
8P GAIN WILD-TYPE	94	149	62	37

Figure S102. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.066

Table S103. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
8P GAIN MUTATED	50	29	12	25
8P GAIN WILD-TYPE	138	94	81	108

Figure S103. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0344 (Fisher's exact test), Q value = 0.051

Table S104. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
8P GAIN MUTATED	44	23	14	25	9
8P GAIN WILD-TYPE	120	57	92	108	38

Figure S104. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.026

Table S105. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
8Q GAIN MUTATED	1	8	2	0
8Q GAIN WILD-TYPE	14	9	12	7

Figure S105. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0303 (Fisher's exact test), Q value = 0.046

Table S106. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
8Q GAIN MUTATED	4	5	0	0	2
8Q GAIN WILD-TYPE	10	4	7	7	14

Figure S106. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S107. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
8Q GAIN MUTATED	106	6	42	5
8Q GAIN WILD-TYPE	102	172	57	49

Figure S107. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.025

Table S108. Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
8Q GAIN MUTATED	9	13	15	23	31	16	18
8Q GAIN WILD-TYPE	30	68	37	33	53	52	35

Figure S108. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S109. Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
8Q GAIN MUTATED	14	55	39	17
8Q GAIN WILD-TYPE	94	127	54	33

Figure S109. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S110. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
8Q GAIN MUTATED	81	31	18	29
8Q GAIN WILD-TYPE	107	92	75	104

Figure S110. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
8Q GAIN MUTATED	53	10	18	8	37	23	10
8Q GAIN WILD-TYPE	70	43	29	57	71	43	65

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S112. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
8Q GAIN MUTATED	74	24	16	31	11
8Q GAIN WILD-TYPE	90	56	90	102	36

Figure S112. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00832 (Fisher's exact test), Q value = 0.014

Table S113. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
8Q GAIN MUTATED	60	65	31
8Q GAIN WILD-TYPE	158	107	109

Figure S113. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0047

Table S114. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
8Q GAIN MUTATED	53	24	25	24
8Q GAIN WILD-TYPE	63	74	67	68

Figure S114. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00764 (Fisher's exact test), Q value = 0.013

Table S115. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
8Q GAIN MUTATED	66	34	26
8Q GAIN WILD-TYPE	97	98	77

Figure S115. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0013

Table S116. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
9P GAIN MUTATED	18	3	1	0
9P GAIN WILD-TYPE	190	175	98	54

Figure S116. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.0366 (Fisher's exact test), Q value = 0.054

Table S117. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
9P GAIN MUTATED	12	4	4
9P GAIN WILD-TYPE	142	74	189

Figure S117. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.00062

Table S118. Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
9P GAIN MUTATED	0	0	1	10	5	3	2
9P GAIN WILD-TYPE	39	81	51	46	79	65	51

Figure S118. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00476 (Fisher's exact test), Q value = 0.0083

Table S119. Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
9P GAIN MUTATED	0	12	8	1
9P GAIN WILD-TYPE	108	170	85	49

Figure S119. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.008

Table S120. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
9P GAIN MUTATED	15	2	4	1
9P GAIN WILD-TYPE	173	121	89	132

Figure S120. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.043

Table S121. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
9P GAIN MUTATED	10	0	2	1	7	2	0
9P GAIN WILD-TYPE	113	53	45	64	101	64	75

Figure S121. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.00246 (Fisher's exact test), Q value = 0.0046

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
9P GAIN MUTATED	16	2	2	2	0
9P GAIN WILD-TYPE	148	78	104	131	47

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

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0208 (Fisher's exact test), Q value = 0.033

Table S123. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
9P GAIN MUTATED	7	13	2
9P GAIN WILD-TYPE	211	159	138

Figure S123. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0433 (Fisher's exact test), Q value = 0.062

Table S124. Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
9Q GAIN MUTATED	0	4	5	0
9Q GAIN WILD-TYPE	108	178	88	50

Figure S124. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.051

Table S125. Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
9Q GAIN MUTATED	8	1	0	1	0
9Q GAIN WILD-TYPE	156	79	106	132	47

Figure S125. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.0087

Table S126. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
10P GAIN MUTATED	2	2	9	1
10P GAIN WILD-TYPE	13	15	5	6

Figure S126. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.051

Table S127. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
10P GAIN MUTATED	53	26	26	11
10P GAIN WILD-TYPE	155	152	73	43

Figure S127. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.051

Table S128. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
10P GAIN MUTATED	6	25	6	11	12	17	16
10P GAIN WILD-TYPE	33	56	46	45	72	51	37

Figure S128. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.051

Table S129. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
10P GAIN MUTATED	25	27	18	10
10P GAIN WILD-TYPE	91	71	74	82

Figure S129. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00257 (Fisher's exact test), Q value = 0.0047

Table S130. Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
10Q GAIN MUTATED	1	3	9	1
10Q GAIN WILD-TYPE	14	14	5	6

Figure S130. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.053

Table S131. Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
11P GAIN MUTATED	0	4	0	0
11P GAIN WILD-TYPE	15	13	14	7

Figure S131. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S132. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
11P GAIN MUTATED	21	0	1	1
11P GAIN WILD-TYPE	187	178	98	53

Figure S132. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.057

Table S133. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
11P GAIN MUTATED	12	3	4
11P GAIN WILD-TYPE	142	75	189

Figure S133. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.00044

Table S134. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
11P GAIN MUTATED	18	2	0	3
11P GAIN WILD-TYPE	170	121	93	130

Figure S134. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0026

Table S135. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
11P GAIN MUTATED	14	1	1	0	5	2	0
11P GAIN WILD-TYPE	109	52	46	65	103	64	75

Figure S135. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.023

Table S136. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
11P GAIN MUTATED	15	2	1	4	1
11P GAIN WILD-TYPE	149	78	105	129	46

Figure S136. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.019

Table S137. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
11P GAIN MUTATED	7	14	2
11P GAIN WILD-TYPE	211	158	138

Figure S137. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S138. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
11Q GAIN MUTATED	17	0	2	1
11Q GAIN WILD-TYPE	191	178	97	53

Figure S138. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.039

Table S139. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
11Q GAIN MUTATED	11	1	4
11Q GAIN WILD-TYPE	143	77	189

Figure S139. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.0036

Table S140. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
11Q GAIN MUTATED	15	2	0	3
11Q GAIN WILD-TYPE	173	121	93	130

Figure S140. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S141. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
12P GAIN MUTATED	53	4	5	7
12P GAIN WILD-TYPE	155	174	94	47

Figure S141. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S142. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
12P GAIN MUTATED	32	15	8
12P GAIN WILD-TYPE	122	63	185

Figure S142. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0492 (Fisher's exact test), Q value = 0.07

Table S143. Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
12P GAIN MUTATED	10	34	8	5
12P GAIN WILD-TYPE	98	148	85	45

Figure S143. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S144. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
12P GAIN MUTATED	44	8	9	8
12P GAIN WILD-TYPE	144	115	84	125

Figure S144. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S145. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
12P GAIN MUTATED	31	1	10	6	11	3	7
12P GAIN WILD-TYPE	92	52	37	59	97	63	68

Figure S145. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.0026

Table S146. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
12P GAIN MUTATED	33	7	11	8	10
12P GAIN WILD-TYPE	131	73	95	125	37

Figure S146. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S147. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
12P GAIN MUTATED	18	41	10
12P GAIN WILD-TYPE	200	131	130

Figure S147. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00676 (Fisher's exact test), Q value = 0.012

Table S148. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
12P GAIN MUTATED	25	6	9	12
12P GAIN WILD-TYPE	91	92	83	80

Figure S148. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.0018

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
12P GAIN MUTATED	32	7	13
12P GAIN WILD-TYPE	131	125	90

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

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S150. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
12Q GAIN MUTATED	35	4	5	7
12Q GAIN WILD-TYPE	173	174	94	47

Figure S150. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.00121 (Fisher's exact test), Q value = 0.0024

Table S151. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
12Q GAIN MUTATED	20	12	8
12Q GAIN WILD-TYPE	134	66	185

Figure S151. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.0337 (Fisher's exact test), Q value = 0.051

Table S152. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
12Q GAIN MUTATED	27	7	9	8
12Q GAIN WILD-TYPE	161	116	84	125

Figure S152. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.026

Table S153. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
12Q GAIN MUTATED	15	26	10
12Q GAIN WILD-TYPE	203	146	130

Figure S153. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0064 (Fisher's exact test), Q value = 0.011

Table S154. Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
13Q GAIN MUTATED	0	3	0	0	0
13Q GAIN WILD-TYPE	14	6	7	7	16

Figure S154. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S155. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
13Q GAIN MUTATED	28	0	1	1
13Q GAIN WILD-TYPE	180	178	98	53

Figure S155. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00019

Table S156. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
13Q GAIN MUTATED	16	8	2
13Q GAIN WILD-TYPE	138	70	191

Figure S156. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00263 (Fisher's exact test), Q value = 0.0048

Table S157. Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
13Q GAIN MUTATED	0	17	6	3
13Q GAIN WILD-TYPE	108	165	87	47

Figure S157. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S158. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
13Q GAIN MUTATED	26	0	2	2
13Q GAIN WILD-TYPE	162	123	91	131

Figure S158. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S159. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
13Q GAIN MUTATED	26	0	1	0	1	1	1
13Q GAIN WILD-TYPE	97	53	46	65	107	65	74

Figure S159. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S160. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
13Q GAIN MUTATED	23	0	3	2	2
13Q GAIN WILD-TYPE	141	80	103	131	45

Figure S160. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S161. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
13Q GAIN MUTATED	2	26	2
13Q GAIN WILD-TYPE	216	146	138

Figure S161. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.043

Table S162. Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
13Q GAIN MUTATED	12	1	6	6
13Q GAIN WILD-TYPE	104	97	86	86

Figure S162. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.01 (Fisher's exact test), Q value = 0.016

Table S163. Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
13Q GAIN MUTATED	14	2	9
13Q GAIN WILD-TYPE	149	130	94

Figure S163. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S164. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
14Q GAIN MUTATED	28	1	2	5
14Q GAIN WILD-TYPE	180	177	97	49

Figure S164. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.046

Table S165. Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
14Q GAIN MUTATED	19	5	9
14Q GAIN WILD-TYPE	135	73	184

Figure S165. 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 = 2.8e-05

Table S166. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
14Q GAIN MUTATED	26	4	0	6
14Q GAIN WILD-TYPE	162	119	93	127

Figure S166. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0012 (Fisher's exact test), Q value = 0.0023

Table S167. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
14Q GAIN MUTATED	16	1	6	1	8	0	4
14Q GAIN WILD-TYPE	107	52	41	64	100	66	71

Figure S167. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00058

Table S168. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
14Q GAIN MUTATED	21	4	0	7	4
14Q GAIN WILD-TYPE	143	76	106	126	43

Figure S168. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00343 (Fisher's exact test), Q value = 0.0062

Table S169. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
14Q GAIN MUTATED	8	21	7
14Q GAIN WILD-TYPE	210	151	133

Figure S169. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.015

Table S170. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
15Q GAIN MUTATED	10	1	0	0
15Q GAIN WILD-TYPE	198	177	99	54

Figure S170. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S171. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
16P GAIN MUTATED	22	1	1	1
16P GAIN WILD-TYPE	186	177	98	53

Figure S171. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00325 (Fisher's exact test), Q value = 0.0059

Table S172. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
16P GAIN MUTATED	15	0	8
16P GAIN WILD-TYPE	139	78	185

Figure S172. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.00927 (Fisher's exact test), Q value = 0.015

Table S173. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
16P GAIN MUTATED	17	2	2	4
16P GAIN WILD-TYPE	171	121	91	129

Figure S173. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.069

Table S174. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
16P GAIN MUTATED	12	2	2	1	5	3	0
16P GAIN WILD-TYPE	111	51	45	64	103	63	75

Figure S174. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.033

Table S175. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
16P GAIN MUTATED	16	2	3	3	1
16P GAIN WILD-TYPE	148	78	103	130	46

Figure S175. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0478 (Fisher's exact test), Q value = 0.068

Table S176. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
16P GAIN MUTATED	7	14	4
16P GAIN WILD-TYPE	211	158	136

Figure S176. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.063

Table S177. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
16Q GAIN MUTATED	8	1	0	1
16Q GAIN WILD-TYPE	200	177	99	53

Figure S177. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.056

Table S178. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
17P GAIN MUTATED	10	1	1	1
17P GAIN WILD-TYPE	198	177	98	53

Figure S178. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0084 (Fisher's exact test), Q value = 0.014

Table S179. Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
17P GAIN MUTATED	10	1	2	0
17P GAIN WILD-TYPE	178	122	91	133

Figure S179. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.027

Table S180. Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
17P GAIN MUTATED	9	0	1	1	2	0	0
17P GAIN WILD-TYPE	114	53	46	64	106	66	75

Figure S180. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00461 (Fisher's exact test), Q value = 0.0081

Table S181. Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
17P GAIN MUTATED	2	10	1
17P GAIN WILD-TYPE	216	162	139

Figure S181. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0341 (Fisher's exact test), Q value = 0.051

Table S182. Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
17P GAIN MUTATED	7	2	1	0
17P GAIN WILD-TYPE	109	96	91	92

Figure S182. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S183. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
17Q GAIN MUTATED	26	1	2	1
17Q GAIN WILD-TYPE	182	177	97	53

Figure S183. 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 = 2.8e-05

Table S184. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
17Q GAIN MUTATED	21	3	2
17Q GAIN WILD-TYPE	133	75	191

Figure S184. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S185. Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
17Q GAIN MUTATED	1	0	0	5	10	8	1
17Q GAIN WILD-TYPE	38	81	52	51	74	60	52

Figure S185. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S186. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
17Q GAIN MUTATED	23	1	4	2
17Q GAIN WILD-TYPE	165	122	89	131

Figure S186. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S187. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
17Q GAIN MUTATED	19	0	5	1	3	2	0
17Q GAIN WILD-TYPE	104	53	42	64	105	64	75

Figure S187. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S188. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
17Q GAIN MUTATED	22	1	2	3	2
17Q GAIN WILD-TYPE	142	79	104	130	45

Figure S188. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S189. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
17Q GAIN MUTATED	3	24	3
17Q GAIN WILD-TYPE	215	148	137

Figure S189. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0344 (Fisher's exact test), Q value = 0.051

Table S190. Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
17Q GAIN MUTATED	15	3	7
17Q GAIN WILD-TYPE	148	129	96

Figure S190. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S191. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
18P GAIN MUTATED	68	1	2	2
18P GAIN WILD-TYPE	140	177	97	52

Figure S191. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S192. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
18P GAIN MUTATED	41	17	5
18P GAIN WILD-TYPE	113	61	188

Figure S192. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S193. Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
18P GAIN MUTATED	1	1	4	13	22	11	7
18P GAIN WILD-TYPE	38	80	48	43	62	57	46

Figure S193. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00029

Table S194. Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
18P GAIN MUTATED	4	39	12	4
18P GAIN WILD-TYPE	104	143	81	46

Figure S194. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S195. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
18P GAIN MUTATED	59	2	8	4
18P GAIN WILD-TYPE	129	121	85	129

Figure S195. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S196. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
18P GAIN MUTATED	48	1	13	1	7	2	1
18P GAIN WILD-TYPE	75	52	34	64	101	64	74

Figure S196. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S197. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
18P GAIN MUTATED	52	5	6	2	8
18P GAIN WILD-TYPE	112	75	100	131	39

Figure S197. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S198. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
18P GAIN MUTATED	12	59	2
18P GAIN WILD-TYPE	206	113	138

Figure S198. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S199. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
18P GAIN MUTATED	30	3	16	11
18P GAIN WILD-TYPE	86	95	76	81

Figure S199. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S200. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
18P GAIN MUTATED	34	2	24
18P GAIN WILD-TYPE	129	130	79

Figure S200. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S201. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
18Q GAIN MUTATED	41	1	2	2
18Q GAIN WILD-TYPE	167	177	97	52

Figure S201. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S202. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
18Q GAIN MUTATED	24	12	4
18Q GAIN WILD-TYPE	130	66	189

Figure S202. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00019

Table S203. Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
18Q GAIN MUTATED	0	1	1	8	16	6	4
18Q GAIN WILD-TYPE	39	80	51	48	68	62	49

Figure S203. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.019

Table S204. Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
18Q GAIN MUTATED	2	21	10	3
18Q GAIN WILD-TYPE	106	161	83	47

Figure S204. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S205. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
18Q GAIN MUTATED	38	2	3	3
18Q GAIN WILD-TYPE	150	121	90	130

Figure S205. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S206. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
18Q GAIN MUTATED	32	1	4	0	6	2	1
18Q GAIN WILD-TYPE	91	52	43	65	102	64	74

Figure S206. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S207. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
18Q GAIN MUTATED	33	5	2	1	5
18Q GAIN WILD-TYPE	131	75	104	132	42

Figure S207. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S208. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
18Q GAIN MUTATED	10	35	1
18Q GAIN WILD-TYPE	208	137	139

Figure S208. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.0095

Table S209. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
18Q GAIN MUTATED	18	2	9	8
18Q GAIN WILD-TYPE	98	96	83	84

Figure S209. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S210. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
18Q GAIN MUTATED	24	1	12
18Q GAIN WILD-TYPE	139	131	91

Figure S210. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.053

Table S211. Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
19P GAIN MUTATED	0	4	0	0
19P GAIN WILD-TYPE	15	13	14	7

Figure S211. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.045

Table S212. Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
19P GAIN MUTATED	1	3	0	0	0
19P GAIN WILD-TYPE	13	6	7	7	16

Figure S212. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S213. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
19P GAIN MUTATED	53	0	1	1
19P GAIN WILD-TYPE	155	178	98	53

Figure S213. 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 = 2.8e-05

Table S214. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
19P GAIN MUTATED	26	16	8
19P GAIN WILD-TYPE	128	62	185

Figure S214. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00279 (Fisher's exact test), Q value = 0.0051

Table S215. Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
19P GAIN MUTATED	1	3	1	10	14	5	7
19P GAIN WILD-TYPE	38	78	51	46	70	63	46

Figure S215. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S216. Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
19P GAIN MUTATED	2	31	4	4
19P GAIN WILD-TYPE	106	151	89	46

Figure S216. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S217. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
19P GAIN MUTATED	44	3	3	4
19P GAIN WILD-TYPE	144	120	90	129

Figure S217. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S218. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
19P GAIN MUTATED	37	1	3	2	8	2	1
19P GAIN WILD-TYPE	86	52	44	63	100	64	74

Figure S218. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S219. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
19P GAIN MUTATED	37	3	3	5	7
19P GAIN WILD-TYPE	127	77	103	128	40

Figure S219. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S220. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
19P GAIN MUTATED	12	37	6
19P GAIN WILD-TYPE	206	135	134

Figure S220. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S221. Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
19P GAIN MUTATED	26	4	12	5
19P GAIN WILD-TYPE	90	94	80	87

Figure S221. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S222. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
19Q GAIN MUTATED	56	0	1	1
19Q GAIN WILD-TYPE	152	178	98	53

Figure S222. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S223. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
19Q GAIN MUTATED	28	17	7
19Q GAIN WILD-TYPE	126	61	186

Figure S223. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.00306 (Fisher's exact test), Q value = 0.0056

Table S224. Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
19Q GAIN MUTATED	1	3	2	10	15	5	8
19Q GAIN WILD-TYPE	38	78	50	46	69	63	45

Figure S224. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S225. Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
19Q GAIN MUTATED	2	32	4	6
19Q GAIN WILD-TYPE	106	150	89	44

Figure S225. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S226. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
19Q GAIN MUTATED	48	3	4	3
19Q GAIN WILD-TYPE	140	120	89	130

Figure S226. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S227. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
19Q GAIN MUTATED	40	1	6	1	8	1	1
19Q GAIN WILD-TYPE	83	52	41	64	100	65	74

Figure S227. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S228. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
19Q GAIN MUTATED	42	3	3	4	6
19Q GAIN WILD-TYPE	122	77	103	129	41

Figure S228. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S229. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
19Q GAIN MUTATED	9	44	5
19Q GAIN WILD-TYPE	209	128	135

Figure S229. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.00036

Table S230. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
19Q GAIN MUTATED	26	3	12	8
19Q GAIN WILD-TYPE	90	95	80	84

Figure S230. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.031

Table S231. Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
19Q GAIN MUTATED	26	8	15
19Q GAIN WILD-TYPE	137	124	88

Figure S231. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.052

Table S232. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
20P GAIN MUTATED	0	4	0	0
20P GAIN WILD-TYPE	15	13	14	7

Figure S232. 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 = 2.8e-05

Table S233. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
20P GAIN MUTATED	99	3	2	5
20P GAIN WILD-TYPE	109	175	97	49

Figure S233. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S234. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
20P GAIN MUTATED	63	20	18
20P GAIN WILD-TYPE	91	58	175

Figure S234. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S235. Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
20P GAIN MUTATED	1	6	3	17	30	15	13
20P GAIN WILD-TYPE	38	75	49	39	54	53	40

Figure S235. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S236. Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
20P GAIN MUTATED	7	51	19	8
20P GAIN WILD-TYPE	101	131	74	42

Figure S236. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S237. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
20P GAIN MUTATED	76	7	12	14
20P GAIN WILD-TYPE	112	116	81	119

Figure S237. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S238. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
20P GAIN MUTATED	60	4	15	2	14	12	2
20P GAIN WILD-TYPE	63	49	32	63	94	54	73

Figure S238. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S239. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
20P GAIN MUTATED	70	8	7	14	10
20P GAIN WILD-TYPE	94	72	99	119	37

Figure S239. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S240. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
20P GAIN MUTATED	24	72	13
20P GAIN WILD-TYPE	194	100	127

Figure S240. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00159 (Fisher's exact test), Q value = 0.003

Table S241. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
20P GAIN MUTATED	41	14	16	23
20P GAIN WILD-TYPE	75	84	76	69

Figure S241. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S242. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
20P GAIN MUTATED	56	18	20
20P GAIN WILD-TYPE	107	114	83

Figure S242. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.00829 (Fisher's exact test), Q value = 0.014

Table S243. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
20Q GAIN MUTATED	0	5	0	0
20Q GAIN WILD-TYPE	15	12	14	7

Figure S243. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S244. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
20Q GAIN MUTATED	119	3	3	5
20Q GAIN WILD-TYPE	89	175	96	49

Figure S244. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S245. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
20Q GAIN MUTATED	73	22	24
20Q GAIN WILD-TYPE	81	56	169

Figure S245. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S246. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
20Q GAIN MUTATED	1	7	5	22	34	17	14
20Q GAIN WILD-TYPE	38	74	47	34	50	51	39

Figure S246. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S247. Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
20Q GAIN MUTATED	8	62	22	8
20Q GAIN WILD-TYPE	100	120	71	42

Figure S247. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S248. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
20Q GAIN MUTATED	91	8	14	17
20Q GAIN WILD-TYPE	97	115	79	116

Figure S248. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S249. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
20Q GAIN MUTATED	69	4	19	3	18	14	3
20Q GAIN WILD-TYPE	54	49	28	62	90	52	72

Figure S249. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S250. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
20Q GAIN MUTATED	84	8	10	17	10
20Q GAIN WILD-TYPE	80	72	96	116	37

Figure S250. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S251. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
20Q GAIN MUTATED	30	82	17
20Q GAIN WILD-TYPE	188	90	123

Figure S251. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S252. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
20Q GAIN MUTATED	52	15	19	25
20Q GAIN WILD-TYPE	64	83	73	67

Figure S252. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S253. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
20Q GAIN MUTATED	64	22	25
20Q GAIN WILD-TYPE	99	110	78

Figure S253. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S254. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
21Q GAIN MUTATED	38	1	0	0
21Q GAIN WILD-TYPE	170	177	99	54

Figure S254. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00023

Table S255. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
21Q GAIN MUTATED	20	11	5
21Q GAIN WILD-TYPE	134	67	188

Figure S255. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00038

Table S256. Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
21Q GAIN MUTATED	0	1	0	10	10	6	5
21Q GAIN WILD-TYPE	39	80	52	46	74	62	48

Figure S256. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S257. Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
21Q GAIN MUTATED	0	21	8	3
21Q GAIN WILD-TYPE	108	161	85	47

Figure S257. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S258. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
21Q GAIN MUTATED	31	1	3	4
21Q GAIN WILD-TYPE	157	122	90	129

Figure S258. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S259. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
21Q GAIN MUTATED	24	0	7	1	3	1	3
21Q GAIN WILD-TYPE	99	53	40	64	105	65	72

Figure S259. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S260. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
21Q GAIN MUTATED	29	0	2	3	5
21Q GAIN WILD-TYPE	135	80	104	130	42

Figure S260. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S261. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
21Q GAIN MUTATED	5	30	4
21Q GAIN WILD-TYPE	213	142	136

Figure S261. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.0073

Table S262. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
21Q GAIN MUTATED	18	3	10	4
21Q GAIN WILD-TYPE	98	95	82	88

Figure S262. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.064

Table S263. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
21Q GAIN MUTATED	15	6	14
21Q GAIN WILD-TYPE	148	126	89

Figure S263. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S264. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
22Q GAIN MUTATED	27	0	1	2
22Q GAIN WILD-TYPE	181	178	98	52

Figure S264. 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 = 2.8e-05

Table S265. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
22Q GAIN MUTATED	23	3	1
22Q GAIN WILD-TYPE	131	75	192

Figure S265. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S266. Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
22Q GAIN MUTATED	0	0	1	7	13	4	1
22Q GAIN WILD-TYPE	39	81	51	49	71	64	52

Figure S266. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S267. Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
22Q GAIN MUTATED	1	24	1	0
22Q GAIN WILD-TYPE	107	158	92	50

Figure S267. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S268. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
22Q GAIN MUTATED	26	0	4	0
22Q GAIN WILD-TYPE	162	123	89	133

Figure S268. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S269. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
22Q GAIN MUTATED	15	0	12	0	3	0	0
22Q GAIN WILD-TYPE	108	53	35	65	105	66	75

Figure S269. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S270. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
22Q GAIN MUTATED	18	0	7	1	3
22Q GAIN WILD-TYPE	146	80	99	132	44

Figure S270. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S271. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
22Q GAIN MUTATED	1	27	1
22Q GAIN WILD-TYPE	217	145	139

Figure S271. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S272. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
22Q GAIN MUTATED	12	1	1	13
22Q GAIN WILD-TYPE	104	97	91	79

Figure S272. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S273. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
22Q GAIN MUTATED	21	1	5
22Q GAIN WILD-TYPE	142	131	98

Figure S273. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S274. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
XP GAIN MUTATED	34	2	20	7
XP GAIN WILD-TYPE	174	176	79	47

Figure S274. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0458 (Fisher's exact test), Q value = 0.065

Table S275. Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
XP GAIN MUTATED	22	9	7	8
XP GAIN WILD-TYPE	94	89	85	84

Figure S275. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S276. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
XQ GAIN MUTATED	37	2	19	6
XQ GAIN WILD-TYPE	171	176	80	48

Figure S276. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.008

Table S277. Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
XQ GAIN MUTATED	24	11	7	5
XQ GAIN WILD-TYPE	92	87	85	87

Figure S277. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S278. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
1P LOSS MUTATED	26	0	0	1
1P LOSS WILD-TYPE	182	178	99	53

Figure S278. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S279. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
1P LOSS MUTATED	18	5	1
1P LOSS WILD-TYPE	136	73	192

Figure S279. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.068

Table S280. Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
1P LOSS MUTATED	0	0	2	5	5	2	4
1P LOSS WILD-TYPE	39	81	50	51	79	66	49

Figure S280. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S281. Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
1P LOSS MUTATED	0	16	0	2
1P LOSS WILD-TYPE	108	166	93	48

Figure S281. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S282. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
1P LOSS MUTATED	23	0	3	1
1P LOSS WILD-TYPE	165	123	90	132

Figure S282. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S283. Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
1P LOSS MUTATED	15	0	7	0	5	0	0
1P LOSS WILD-TYPE	108	53	40	65	103	66	75

Figure S283. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.00091

Table S284. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
1P LOSS MUTATED	19	1	3	2	2
1P LOSS WILD-TYPE	145	79	103	131	45

Figure S284. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S285. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
1P LOSS MUTATED	3	23	1
1P LOSS WILD-TYPE	215	149	139

Figure S285. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.06

Table S286. Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
1P LOSS MUTATED	15	3	6
1P LOSS WILD-TYPE	148	129	97

Figure S286. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S287. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
1Q LOSS MUTATED	16	0	0	0
1Q LOSS WILD-TYPE	192	178	99	54

Figure S287. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 0.00635 (Fisher's exact test), Q value = 0.011

Table S288. Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
1Q LOSS MUTATED	9	4	1
1Q LOSS WILD-TYPE	145	74	192

Figure S288. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.038

Table S289. Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
1Q LOSS MUTATED	0	8	0	1
1Q LOSS WILD-TYPE	108	174	93	49

Figure S289. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00092 (Fisher's exact test), Q value = 0.0018

Table S290. Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
1Q LOSS MUTATED	13	0	2	1
1Q LOSS WILD-TYPE	175	123	91	132

Figure S290. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00108 (Fisher's exact test), Q value = 0.0021

Table S291. Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
1Q LOSS MUTATED	8	0	5	0	3	0	0
1Q LOSS WILD-TYPE	115	53	42	65	105	66	75

Figure S291. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0288 (Fisher's exact test), Q value = 0.044

Table S292. Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
1Q LOSS MUTATED	11	0	2	2	1
1Q LOSS WILD-TYPE	153	80	104	131	46

Figure S292. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00026 (Fisher's exact test), Q value = 0.00057

Table S293. Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
1Q LOSS MUTATED	2	13	1
1Q LOSS WILD-TYPE	216	159	139

Figure S293. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S294. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
2P LOSS MUTATED	12	0	0	0
2P LOSS WILD-TYPE	196	178	99	54

Figure S294. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0014

Table S295. Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
2P LOSS MUTATED	11	0	0	1
2P LOSS WILD-TYPE	177	123	93	132

Figure S295. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.06

Table S296. Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
2P LOSS MUTATED	7	0	1	0	4	0	0
2P LOSS WILD-TYPE	116	53	46	65	104	66	75

Figure S296. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S297. Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
2Q LOSS MUTATED	18	0	0	0
2Q LOSS WILD-TYPE	190	178	99	54

Figure S297. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.06

Table S298. Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
2Q LOSS MUTATED	9	5	3
2Q LOSS WILD-TYPE	145	73	190

Figure S298. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S299. Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
2Q LOSS MUTATED	16	0	0	2
2Q LOSS WILD-TYPE	172	123	93	131

Figure S299. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0072 (Fisher's exact test), Q value = 0.012

Table S300. Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
2Q LOSS MUTATED	10	0	1	0	6	1	0
2Q LOSS WILD-TYPE	113	53	46	65	102	65	75

Figure S300. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00873 (Fisher's exact test), Q value = 0.015

Table S301. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
2Q LOSS MUTATED	13	2	1	2	0
2Q LOSS WILD-TYPE	151	78	105	131	47

Figure S301. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0426 (Fisher's exact test), Q value = 0.061

Table S302. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
2Q LOSS MUTATED	4	11	3
2Q LOSS WILD-TYPE	214	161	137

Figure S302. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.054

Table S303. Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
3P LOSS MUTATED	0	4	0	0
3P LOSS WILD-TYPE	15	13	14	7

Figure S303. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00071 (Fisher's exact test), Q value = 0.0014

Table S304. Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
3P LOSS MUTATED	0	4	0	0	0
3P LOSS WILD-TYPE	14	5	7	7	16

Figure S304. 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 = 2.8e-05

Table S305. Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
3P LOSS MUTATED	49	0	0	3
3P LOSS WILD-TYPE	159	178	99	51

Figure S305. 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 = 2.8e-05

Table S306. Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
3P LOSS MUTATED	28	11	4
3P LOSS WILD-TYPE	126	67	189

Figure S306. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.0012

Table S307. Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
3P LOSS MUTATED	2	1	3	8	18	7	4
3P LOSS WILD-TYPE	37	80	49	48	66	61	49

Figure S307. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S308. Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
3P LOSS MUTATED	1	30	10	2
3P LOSS WILD-TYPE	107	152	83	48

Figure S308. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S309. Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
3P LOSS MUTATED	43	3	3	2
3P LOSS WILD-TYPE	145	120	90	131

Figure S309. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S310. Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
3P LOSS MUTATED	36	0	6	0	7	2	0
3P LOSS WILD-TYPE	87	53	41	65	101	64	75

Figure S310. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S311. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
3P LOSS MUTATED	37	3	5	3	2
3P LOSS WILD-TYPE	127	77	101	130	45

Figure S311. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S312. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
3P LOSS MUTATED	12	36	2
3P LOSS WILD-TYPE	206	136	138

Figure S312. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S313. Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
3P LOSS MUTATED	28	3	10
3P LOSS WILD-TYPE	135	129	93

Figure S313. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.0361 (Fisher's exact test), Q value = 0.053

Table S314. Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
3Q LOSS MUTATED	0	4	0	0
3Q LOSS WILD-TYPE	15	13	14	7

Figure S314. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.0014

Table S315. Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
3Q LOSS MUTATED	0	4	0	0	0
3Q LOSS WILD-TYPE	14	5	7	7	16

Figure S315. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S316. Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
3Q LOSS MUTATED	28	0	0	3
3Q LOSS WILD-TYPE	180	178	99	51

Figure S316. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S317. Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
3Q LOSS MUTATED	19	3	3
3Q LOSS WILD-TYPE	135	75	190

Figure S317. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.051

Table S318. Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
3Q LOSS MUTATED	0	1	3	4	11	5	3
3Q LOSS WILD-TYPE	39	80	49	52	73	63	50

Figure S318. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.001

Table S319. Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
3Q LOSS MUTATED	0	20	5	2
3Q LOSS WILD-TYPE	108	162	88	48

Figure S319. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S320. Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
3Q LOSS MUTATED	26	1	1	2
3Q LOSS WILD-TYPE	162	122	92	131

Figure S320. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S321. Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
3Q LOSS MUTATED	20	0	4	0	4	2	0
3Q LOSS WILD-TYPE	103	53	43	65	104	64	75

Figure S321. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.0015

Table S322. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
3Q LOSS MUTATED	20	1	3	3	2
3Q LOSS WILD-TYPE	144	79	103	130	45

Figure S322. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00016 (Fisher's exact test), Q value = 0.00036

Table S323. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
3Q LOSS MUTATED	7	20	2
3Q LOSS WILD-TYPE	211	152	138

Figure S323. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0468 (Fisher's exact test), Q value = 0.066

Table S324. Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
3Q LOSS MUTATED	14	3	8
3Q LOSS WILD-TYPE	149	129	95

Figure S324. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 0.00366 (Fisher's exact test), Q value = 0.0065

Table S325. Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
4P LOSS MUTATED	1	7	0	0
4P LOSS WILD-TYPE	14	10	14	7

Figure S325. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.0034

Table S326. Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
4P LOSS MUTATED	3	5	0	0	0
4P LOSS WILD-TYPE	11	4	7	7	16

Figure S326. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S327. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
4P LOSS MUTATED	102	1	1	2
4P LOSS WILD-TYPE	106	177	98	52

Figure S327. 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 = 2.8e-05

Table S328. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
4P LOSS MUTATED	62	23	10
4P LOSS WILD-TYPE	92	55	183

Figure S328. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S329. Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
4P LOSS MUTATED	3	1	5	21	31	10	14
4P LOSS WILD-TYPE	36	80	47	35	53	58	39

Figure S329. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S330. Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
4P LOSS MUTATED	4	55	17	9
4P LOSS WILD-TYPE	104	127	76	41

Figure S330. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S331. Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
4P LOSS MUTATED	83	5	11	7
4P LOSS WILD-TYPE	105	118	82	126

Figure S331. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S332. Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
4P LOSS MUTATED	63	2	15	2	18	5	1
4P LOSS WILD-TYPE	60	51	32	63	90	61	74

Figure S332. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S333. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
4P LOSS MUTATED	78	7	4	7	8
4P LOSS WILD-TYPE	86	73	102	126	39

Figure S333. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S334. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
4P LOSS MUTATED	26	73	5
4P LOSS WILD-TYPE	192	99	135

Figure S334. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S335. Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
4P LOSS MUTATED	48	8	22	16
4P LOSS WILD-TYPE	68	90	70	76

Figure S335. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S336. Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
4P LOSS MUTATED	52	12	30
4P LOSS WILD-TYPE	111	120	73

Figure S336. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.061

Table S337. Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
4Q LOSS MUTATED	1	5	0	0
4Q LOSS WILD-TYPE	14	12	14	7

Figure S337. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00793 (Fisher's exact test), Q value = 0.013

Table S338. Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
4Q LOSS MUTATED	2	4	0	0	0
4Q LOSS WILD-TYPE	12	5	7	7	16

Figure S338. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S339. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
4Q LOSS MUTATED	101	0	1	2
4Q LOSS WILD-TYPE	107	178	98	52

Figure S339. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S340. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
4Q LOSS MUTATED	60	25	8
4Q LOSS WILD-TYPE	94	53	185

Figure S340. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S341. Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
4Q LOSS MUTATED	3	2	4	16	32	11	16
4Q LOSS WILD-TYPE	36	79	48	40	52	57	37

Figure S341. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S342. Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
4Q LOSS MUTATED	4	52	18	10
4Q LOSS WILD-TYPE	104	130	75	40

Figure S342. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S343. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
4Q LOSS MUTATED	84	5	8	7
4Q LOSS WILD-TYPE	104	118	85	126

Figure S343. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S344. Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
4Q LOSS MUTATED	65	2	12	2	17	6	0
4Q LOSS WILD-TYPE	58	51	35	63	91	60	75

Figure S344. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S345. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
4Q LOSS MUTATED	73	7	5	7	10
4Q LOSS WILD-TYPE	91	73	101	126	37

Figure S345. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S346. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
4Q LOSS MUTATED	26	72	4
4Q LOSS WILD-TYPE	192	100	136

Figure S346. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S347. Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
4Q LOSS MUTATED	46	8	22	16
4Q LOSS WILD-TYPE	70	90	70	76

Figure S347. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S348. Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
4Q LOSS MUTATED	50	11	31
4Q LOSS WILD-TYPE	113	121	72

Figure S348. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 0.0429 (Fisher's exact test), Q value = 0.062

Table S349. Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
5P LOSS MUTATED	1	5	0	0
5P LOSS WILD-TYPE	14	12	14	7

Figure S349. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.059

Table S350. Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
5P LOSS MUTATED	3	3	0	0	0
5P LOSS WILD-TYPE	11	6	7	7	16

Figure S350. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S351. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
5P LOSS MUTATED	51	0	0	2
5P LOSS WILD-TYPE	157	178	99	52

Figure S351. 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 = 2.8e-05

Table S352. Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
5P LOSS MUTATED	33	7	3
5P LOSS WILD-TYPE	121	71	190

Figure S352. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.00073

Table S353. Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
5P LOSS MUTATED	1	2	2	13	14	6	6
5P LOSS WILD-TYPE	38	79	50	43	70	62	47

Figure S353. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S354. Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
5P LOSS MUTATED	1	29	9	5
5P LOSS WILD-TYPE	107	153	84	45

Figure S354. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S355. Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
5P LOSS MUTATED	40	4	5	4
5P LOSS WILD-TYPE	148	119	88	129

Figure S355. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S356. Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
5P LOSS MUTATED	32	0	8	1	8	4	0
5P LOSS WILD-TYPE	91	53	39	64	100	62	75

Figure S356. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S357. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
5P LOSS MUTATED	36	3	5	4	4
5P LOSS WILD-TYPE	128	77	101	129	43

Figure S357. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S358. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
5P LOSS MUTATED	12	38	2
5P LOSS WILD-TYPE	206	134	138

Figure S358. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S359. Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
5P LOSS MUTATED	25	3	7	6
5P LOSS WILD-TYPE	91	95	85	86

Figure S359. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00048

Table S360. Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
5P LOSS MUTATED	24	3	14
5P LOSS WILD-TYPE	139	129	89

Figure S360. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.018

Table S361. Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
5Q LOSS MUTATED	1	6	0	0
5Q LOSS WILD-TYPE	14	11	14	7

Figure S361. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.016

Table S362. Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
5Q LOSS MUTATED	3	4	0	0	0
5Q LOSS WILD-TYPE	11	5	7	7	16

Figure S362. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S363. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
5Q LOSS MUTATED	71	0	0	2
5Q LOSS WILD-TYPE	137	178	99	52

Figure S363. 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 = 2.8e-05

Table S364. Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
5Q LOSS MUTATED	48	10	3
5Q LOSS WILD-TYPE	106	68	190

Figure S364. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S365. Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
5Q LOSS MUTATED	1	2	3	13	19	9	11
5Q LOSS WILD-TYPE	38	79	49	43	65	59	42

Figure S365. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S366. Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
5Q LOSS MUTATED	0	39	12	7
5Q LOSS WILD-TYPE	108	143	81	43

Figure S366. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S367. Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
5Q LOSS MUTATED	59	3	6	5
5Q LOSS WILD-TYPE	129	120	87	128

Figure S367. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S368. Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
5Q LOSS MUTATED	49	0	7	1	11	5	0
5Q LOSS WILD-TYPE	74	53	40	64	97	61	75

Figure S368. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S369. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
5Q LOSS MUTATED	51	3	6	4	8
5Q LOSS WILD-TYPE	113	77	100	129	39

Figure S369. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S370. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
5Q LOSS MUTATED	15	54	3
5Q LOSS WILD-TYPE	203	118	137

Figure S370. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S371. Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
5Q LOSS MUTATED	36	3	10	9
5Q LOSS WILD-TYPE	80	95	82	83

Figure S371. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S372. Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
5Q LOSS MUTATED	33	5	20
5Q LOSS WILD-TYPE	130	127	83

Figure S372. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.046

Table S373. Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
6P LOSS MUTATED	1	3	0	0	0
6P LOSS WILD-TYPE	13	6	7	7	16

Figure S373. 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 = 2.8e-05

Table S374. Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
6P LOSS MUTATED	19	0	0	1
6P LOSS WILD-TYPE	189	178	99	53

Figure S374. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00069

Table S375. Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
6P LOSS MUTATED	10	4	0
6P LOSS WILD-TYPE	144	74	193

Figure S375. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'RPPA_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.055

Table S376. Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
6P LOSS MUTATED	1	0	1	3	7	2	0
6P LOSS WILD-TYPE	38	81	51	53	77	66	53

Figure S376. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S377. Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
6P LOSS MUTATED	17	1	1	1
6P LOSS WILD-TYPE	171	122	92	132

Figure S377. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S378. Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
6P LOSS MUTATED	14	1	2	0	2	1	0
6P LOSS WILD-TYPE	109	52	45	65	106	65	75

Figure S378. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.00352 (Fisher's exact test), Q value = 0.0063

Table S379. Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
6P LOSS MUTATED	13	1	1	1	2
6P LOSS WILD-TYPE	151	79	105	132	45

Figure S379. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00083

Table S380. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
6P LOSS MUTATED	5	13	0
6P LOSS WILD-TYPE	213	159	140

Figure S380. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S381. Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
6P LOSS MUTATED	10	1	2	1
6P LOSS WILD-TYPE	106	97	90	91

Figure S381. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0294 (Fisher's exact test), Q value = 0.045

Table S382. Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
6Q LOSS MUTATED	1	3	0	0	0
6Q LOSS WILD-TYPE	13	6	7	7	16

Figure S382. 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 = 2.8e-05

Table S383. Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
6Q LOSS MUTATED	24	0	0	1
6Q LOSS WILD-TYPE	184	178	99	53

Figure S383. 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 = 2.8e-05

Table S384. Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
6Q LOSS MUTATED	14	5	0
6Q LOSS WILD-TYPE	140	73	193

Figure S384. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CNMF'

P value = 0.0464 (Fisher's exact test), Q value = 0.066

Table S385. Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
6Q LOSS MUTATED	1	0	1	4	8	2	2
6Q LOSS WILD-TYPE	38	81	51	52	76	66	51

Figure S385. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S386. Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
6Q LOSS MUTATED	22	1	1	1
6Q LOSS WILD-TYPE	166	122	92	132

Figure S386. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S387. Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
6Q LOSS MUTATED	20	1	2	0	2	0	0
6Q LOSS WILD-TYPE	103	52	45	65	106	66	75

Figure S387. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00033 (Fisher's exact test), Q value = 0.00069

Table S388. Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
6Q LOSS MUTATED	17	2	1	1	2
6Q LOSS WILD-TYPE	147	78	105	132	45

Figure S388. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S389. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
6Q LOSS MUTATED	5	18	0
6Q LOSS WILD-TYPE	213	154	140

Figure S389. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00881 (Fisher's exact test), Q value = 0.015

Table S390. Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
6Q LOSS MUTATED	12	1	4	2
6Q LOSS WILD-TYPE	104	97	88	90

Figure S390. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.022

Table S391. Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
6Q LOSS MUTATED	10	1	8
6Q LOSS WILD-TYPE	153	131	95

Figure S391. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.053

Table S392. Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
7P LOSS MUTATED	0	4	0	0
7P LOSS WILD-TYPE	15	13	14	7

Figure S392. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S393. Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
7P LOSS MUTATED	42	3	0	0
7P LOSS WILD-TYPE	166	175	99	54

Figure S393. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S394. Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
7P LOSS MUTATED	21	13	6
7P LOSS WILD-TYPE	133	65	187

Figure S394. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.00202 (Fisher's exact test), Q value = 0.0038

Table S395. Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
7P LOSS MUTATED	1	2	1	8	14	4	7
7P LOSS WILD-TYPE	38	79	51	48	70	64	46

Figure S395. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0039 (Fisher's exact test), Q value = 0.0069

Table S396. Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
7P LOSS MUTATED	2	24	6	5
7P LOSS WILD-TYPE	106	158	87	45

Figure S396. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S397. Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
7P LOSS MUTATED	39	2	1	3
7P LOSS WILD-TYPE	149	121	92	130

Figure S397. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S398. Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
7P LOSS MUTATED	31	0	2	0	8	4	0
7P LOSS WILD-TYPE	92	53	45	65	100	62	75

Figure S398. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S399. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
7P LOSS MUTATED	31	2	2	6	4
7P LOSS WILD-TYPE	133	78	104	127	43

Figure S399. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S400. Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
7P LOSS MUTATED	11	31	3
7P LOSS WILD-TYPE	207	141	137

Figure S400. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S401. Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
7Q LOSS MUTATED	45	0	0	0
7Q LOSS WILD-TYPE	163	178	99	54

Figure S401. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S402. Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
7Q LOSS MUTATED	26	12	3
7Q LOSS WILD-TYPE	128	66	190

Figure S402. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S403. Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
7Q LOSS MUTATED	0	1	2	7	17	4	6
7Q LOSS WILD-TYPE	39	80	50	49	67	64	47

Figure S403. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00093 (Fisher's exact test), Q value = 0.0018

Table S404. Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
7Q LOSS MUTATED	1	24	7	5
7Q LOSS WILD-TYPE	107	158	86	45

Figure S404. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S405. Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
7Q LOSS MUTATED	43	0	1	1
7Q LOSS WILD-TYPE	145	123	92	132

Figure S405. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S406. Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
7Q LOSS MUTATED	34	0	4	0	5	2	0
7Q LOSS WILD-TYPE	89	53	43	65	103	64	75

Figure S406. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S407. Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
7Q LOSS MUTATED	37	1	2	2	3
7Q LOSS WILD-TYPE	127	79	104	131	44

Figure S407. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S408. Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
7Q LOSS MUTATED	8	36	1
7Q LOSS WILD-TYPE	210	136	139

Figure S408. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S409. Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
7Q LOSS MUTATED	24	2	6	7
7Q LOSS WILD-TYPE	92	96	86	85

Figure S409. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00305 (Fisher's exact test), Q value = 0.0055

Table S410. Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
7Q LOSS MUTATED	21	4	14
7Q LOSS WILD-TYPE	142	128	89

Figure S410. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00872 (Fisher's exact test), Q value = 0.015

Table S411. Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
8P LOSS MUTATED	0	5	0	0
8P LOSS WILD-TYPE	15	12	14	7

Figure S411. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S412. Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
8P LOSS MUTATED	0	5	0	0	0
8P LOSS WILD-TYPE	14	4	7	7	16

Figure S412. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S413. Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
8P LOSS MUTATED	75	1	1	1
8P LOSS WILD-TYPE	133	177	98	53

Figure S413. 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 = 2.8e-05

Table S414. Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
8P LOSS MUTATED	48	19	2
8P LOSS WILD-TYPE	106	59	191

Figure S414. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S415. Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
8P LOSS MUTATED	1	2	5	11	24	11	11
8P LOSS WILD-TYPE	38	79	47	45	60	57	42

Figure S415. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S416. Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
8P LOSS MUTATED	1	47	10	7
8P LOSS WILD-TYPE	107	135	83	43

Figure S416. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S417. Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
8P LOSS MUTATED	64	2	9	2
8P LOSS WILD-TYPE	124	121	84	131

Figure S417. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S418. Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
8P LOSS MUTATED	56	0	11	1	7	1	1
8P LOSS WILD-TYPE	67	53	36	64	101	65	74

Figure S418. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S419. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
8P LOSS MUTATED	59	2	6	3	5
8P LOSS WILD-TYPE	105	78	100	130	42

Figure S419. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S420. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
8P LOSS MUTATED	9	63	3
8P LOSS WILD-TYPE	209	109	137

Figure S420. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S421. Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
8P LOSS MUTATED	34	2	13	16
8P LOSS WILD-TYPE	82	96	79	76

Figure S421. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S422. Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
8P LOSS MUTATED	37	4	24
8P LOSS WILD-TYPE	126	128	79

Figure S422. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S423. Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
8Q LOSS MUTATED	20	0	1	1
8Q LOSS WILD-TYPE	188	178	98	53

Figure S423. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S424. Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
8Q LOSS MUTATED	15	5	0
8Q LOSS WILD-TYPE	139	73	193

Figure S424. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'RPPA_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.0051

Table S425. Gene #57: '8q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
8Q LOSS MUTATED	0	1	2	3	12	1	2
8Q LOSS WILD-TYPE	39	80	50	53	72	67	51

Figure S425. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00051 (Fisher's exact test), Q value = 0.001

Table S426. Gene #57: '8q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
8Q LOSS MUTATED	1	18	1	1
8Q LOSS WILD-TYPE	107	164	92	49

Figure S426. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S427. Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
8Q LOSS MUTATED	18	0	3	1
8Q LOSS WILD-TYPE	170	123	90	132

Figure S427. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S428. Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
8Q LOSS MUTATED	18	0	2	0	1	0	1
8Q LOSS WILD-TYPE	105	53	45	65	107	66	74

Figure S428. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S429. Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
8Q LOSS MUTATED	18	0	2	1	0
8Q LOSS WILD-TYPE	146	80	104	132	47

Figure S429. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S430. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
8Q LOSS MUTATED	1	19	1
8Q LOSS WILD-TYPE	217	153	139

Figure S430. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S431. Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
8Q LOSS MUTATED	14	0	1	4
8Q LOSS WILD-TYPE	102	98	91	88

Figure S431. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0024

Table S432. Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
8Q LOSS MUTATED	12	0	7
8Q LOSS WILD-TYPE	151	132	96

Figure S432. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00126 (Fisher's exact test), Q value = 0.0024

Table S433. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
9P LOSS MUTATED	1	8	0	0
9P LOSS WILD-TYPE	14	9	14	7

Figure S433. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S434. Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
9P LOSS MUTATED	2	7	0	0	0
9P LOSS WILD-TYPE	12	2	7	7	16

Figure S434. 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 = 2.8e-05

Table S435. Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
9P LOSS MUTATED	94	1	0	4
9P LOSS WILD-TYPE	114	177	99	50

Figure S435. 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 = 2.8e-05

Table S436. Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
9P LOSS MUTATED	53	21	10
9P LOSS WILD-TYPE	101	57	183

Figure S436. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S437. Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
9P LOSS MUTATED	4	2	6	12	26	10	13
9P LOSS WILD-TYPE	35	79	46	44	58	58	40

Figure S437. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S438. Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
9P LOSS MUTATED	5	44	17	7
9P LOSS WILD-TYPE	103	138	76	43

Figure S438. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S439. Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
9P LOSS MUTATED	73	5	8	13
9P LOSS WILD-TYPE	115	118	85	120

Figure S439. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S440. Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
9P LOSS MUTATED	56	0	17	2	12	11	1
9P LOSS WILD-TYPE	67	53	30	63	96	55	74

Figure S440. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S441. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
9P LOSS MUTATED	65	5	5	12	9
9P LOSS WILD-TYPE	99	75	101	121	38

Figure S441. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S442. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
9P LOSS MUTATED	19	65	12
9P LOSS WILD-TYPE	199	107	128

Figure S442. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00384 (Fisher's exact test), Q value = 0.0069

Table S443. Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
9P LOSS MUTATED	37	13	18	14
9P LOSS WILD-TYPE	79	85	74	78

Figure S443. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.029

Table S444. Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
9P LOSS MUTATED	42	17	23
9P LOSS WILD-TYPE	121	115	80

Figure S444. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S445. Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
9Q LOSS MUTATED	0	9	0	0
9Q LOSS WILD-TYPE	15	8	14	7

Figure S445. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S446. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
9Q LOSS MUTATED	2	7	0	0	0
9Q LOSS WILD-TYPE	12	2	7	7	16

Figure S446. 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 = 2.8e-05

Table S447. Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
9Q LOSS MUTATED	111	1	1	4
9Q LOSS WILD-TYPE	97	177	98	50

Figure S447. 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 = 2.8e-05

Table S448. Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
9Q LOSS MUTATED	61	25	15
9Q LOSS WILD-TYPE	93	53	178

Figure S448. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S449. Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
9Q LOSS MUTATED	5	2	6	19	30	14	13
9Q LOSS WILD-TYPE	34	79	46	37	54	54	40

Figure S449. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S450. Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
9Q LOSS MUTATED	7	54	21	7
9Q LOSS WILD-TYPE	101	128	72	43

Figure S450. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S451. Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
9Q LOSS MUTATED	87	8	8	14
9Q LOSS WILD-TYPE	101	115	85	119

Figure S451. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S452. Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
9Q LOSS MUTATED	68	0	17	3	15	13	1
9Q LOSS WILD-TYPE	55	53	30	62	93	53	74

Figure S452. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S453. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
9Q LOSS MUTATED	79	6	5	14	10
9Q LOSS WILD-TYPE	85	74	101	119	37

Figure S453. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S454. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
9Q LOSS MUTATED	27	74	13
9Q LOSS WILD-TYPE	191	98	127

Figure S454. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S455. Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
9Q LOSS MUTATED	46	14	21	17
9Q LOSS WILD-TYPE	70	84	71	75

Figure S455. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.0025

Table S456. Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
9Q LOSS MUTATED	53	19	26
9Q LOSS WILD-TYPE	110	113	77

Figure S456. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.0358 (Fisher's exact test), Q value = 0.053

Table S457. Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
10P LOSS MUTATED	0	4	0	0
10P LOSS WILD-TYPE	15	13	14	7

Figure S457. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.046

Table S458. Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
10P LOSS MUTATED	1	3	0	0	0
10P LOSS WILD-TYPE	13	6	7	7	16

Figure S458. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S459. Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
10P LOSS MUTATED	43	0	0	1
10P LOSS WILD-TYPE	165	178	99	53

Figure S459. 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 = 2.8e-05

Table S460. Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
10P LOSS MUTATED	26	10	2
10P LOSS WILD-TYPE	128	68	191

Figure S460. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S461. Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
10P LOSS MUTATED	0	0	3	6	15	5	7
10P LOSS WILD-TYPE	39	81	49	50	69	63	46

Figure S461. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S462. Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
10P LOSS MUTATED	0	27	6	3
10P LOSS WILD-TYPE	108	155	87	47

Figure S462. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S463. Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
10P LOSS MUTATED	38	0	3	3
10P LOSS WILD-TYPE	150	123	90	130

Figure S463. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S464. Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
10P LOSS MUTATED	28	0	8	1	4	3	0
10P LOSS WILD-TYPE	95	53	39	64	104	63	75

Figure S464. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S465. Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
10P LOSS MUTATED	33	3	2	1	3
10P LOSS WILD-TYPE	131	77	104	132	44

Figure S465. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S466. Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
10P LOSS MUTATED	8	32	2
10P LOSS WILD-TYPE	210	140	138

Figure S466. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00087 (Fisher's exact test), Q value = 0.0017

Table S467. Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
10P LOSS MUTATED	21	3	13
10P LOSS WILD-TYPE	142	129	90

Figure S467. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S468. Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
10Q LOSS MUTATED	39	0	0	1
10Q LOSS WILD-TYPE	169	178	99	53

Figure S468. 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 = 2.8e-05

Table S469. Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
10Q LOSS MUTATED	22	11	2
10Q LOSS WILD-TYPE	132	67	191

Figure S469. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 0.00655 (Fisher's exact test), Q value = 0.011

Table S470. Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
10Q LOSS MUTATED	0	1	4	4	13	6	6
10Q LOSS WILD-TYPE	39	80	48	52	71	62	47

Figure S470. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S471. Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
10Q LOSS MUTATED	0	25	5	4
10Q LOSS WILD-TYPE	108	157	88	46

Figure S471. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S472. Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
10Q LOSS MUTATED	33	0	3	4
10Q LOSS WILD-TYPE	155	123	90	129

Figure S472. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S473. Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
10Q LOSS MUTATED	25	0	5	1	5	4	0
10Q LOSS WILD-TYPE	98	53	42	64	103	62	75

Figure S473. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S474. Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
10Q LOSS MUTATED	29	3	2	2	3
10Q LOSS WILD-TYPE	135	77	104	131	44

Figure S474. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S475. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
10Q LOSS MUTATED	9	27	3
10Q LOSS WILD-TYPE	209	145	137

Figure S475. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.007

Table S476. Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
10Q LOSS MUTATED	19	3	5	7
10Q LOSS WILD-TYPE	97	95	87	85

Figure S476. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.02

Table S477. Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
10Q LOSS MUTATED	19	4	11
10Q LOSS WILD-TYPE	144	128	92

Figure S477. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S478. Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
11P LOSS MUTATED	71	0	0	5
11P LOSS WILD-TYPE	137	178	99	49

Figure S478. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S479. Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
11P LOSS MUTATED	41	23	7
11P LOSS WILD-TYPE	113	55	186

Figure S479. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00014

Table S480. Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
11P LOSS MUTATED	2	3	5	10	25	8	6
11P LOSS WILD-TYPE	37	78	47	46	59	60	47

Figure S480. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S481. Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
11P LOSS MUTATED	3	42	11	3
11P LOSS WILD-TYPE	105	140	82	47

Figure S481. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S482. Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
11P LOSS MUTATED	57	4	8	7
11P LOSS WILD-TYPE	131	119	85	126

Figure S482. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S483. Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
11P LOSS MUTATED	44	1	11	1	11	8	0
11P LOSS WILD-TYPE	79	52	36	64	97	58	75

Figure S483. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S484. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
11P LOSS MUTATED	54	4	2	9	6
11P LOSS WILD-TYPE	110	76	104	124	41

Figure S484. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S485. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
11P LOSS MUTATED	17	50	8
11P LOSS WILD-TYPE	201	122	132

Figure S485. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00025

Table S486. Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
11P LOSS MUTATED	37	9	14	11
11P LOSS WILD-TYPE	79	89	78	81

Figure S486. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00044

Table S487. Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
11P LOSS MUTATED	44	12	15
11P LOSS WILD-TYPE	119	120	88

Figure S487. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S488. Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
11Q LOSS MUTATED	69	0	0	4
11Q LOSS WILD-TYPE	139	178	99	50

Figure S488. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S489. Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
11Q LOSS MUTATED	40	22	8
11Q LOSS WILD-TYPE	114	56	185

Figure S489. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S490. Gene #63: '11q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
11Q LOSS MUTATED	3	3	5	9	27	9	4
11Q LOSS WILD-TYPE	36	78	47	47	57	59	49

Figure S490. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S491. Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
11Q LOSS MUTATED	4	46	9	1
11Q LOSS WILD-TYPE	104	136	84	49

Figure S491. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S492. Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
11Q LOSS MUTATED	53	4	7	9
11Q LOSS WILD-TYPE	135	119	86	124

Figure S492. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S493. Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
11Q LOSS MUTATED	44	1	10	1	10	7	0
11Q LOSS WILD-TYPE	79	52	37	64	98	59	75

Figure S493. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S494. Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
11Q LOSS MUTATED	55	4	2	10	2
11Q LOSS WILD-TYPE	109	76	104	123	45

Figure S494. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S495. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
11Q LOSS MUTATED	15	49	9
11Q LOSS WILD-TYPE	203	123	131

Figure S495. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S496. Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
11Q LOSS MUTATED	39	10	9	12
11Q LOSS WILD-TYPE	77	88	83	80

Figure S496. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S497. Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
11Q LOSS MUTATED	47	11	12
11Q LOSS WILD-TYPE	116	121	91

Figure S497. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S498. Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
12P LOSS MUTATED	44	0	0	1
12P LOSS WILD-TYPE	164	178	99	53

Figure S498. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S499. Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
12P LOSS MUTATED	24	10	5
12P LOSS WILD-TYPE	130	68	188

Figure S499. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00058

Table S500. Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
12P LOSS MUTATED	1	1	0	7	13	6	8
12P LOSS WILD-TYPE	38	80	52	49	71	62	45

Figure S500. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S501. Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
12P LOSS MUTATED	0	27	5	4
12P LOSS WILD-TYPE	108	155	88	46

Figure S501. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S502. Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
12P LOSS MUTATED	38	1	1	5
12P LOSS WILD-TYPE	150	122	92	128

Figure S502. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S503. Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
12P LOSS MUTATED	28	0	7	1	4	5	0
12P LOSS WILD-TYPE	95	53	40	64	104	61	75

Figure S503. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S504. Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
12P LOSS MUTATED	32	1	3	4	3
12P LOSS WILD-TYPE	132	79	103	129	44

Figure S504. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S505. Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
12P LOSS MUTATED	7	33	3
12P LOSS WILD-TYPE	211	139	137

Figure S505. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0061

Table S506. Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
12P LOSS MUTATED	21	4	5	8
12P LOSS WILD-TYPE	95	94	87	84

Figure S506. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00589 (Fisher's exact test), Q value = 0.01

Table S507. Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
12P LOSS MUTATED	24	5	9
12P LOSS WILD-TYPE	139	127	94

Figure S507. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S508. Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
12Q LOSS MUTATED	39	0	0	1
12Q LOSS WILD-TYPE	169	178	99	53

Figure S508. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S509. Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
12Q LOSS MUTATED	23	8	3
12Q LOSS WILD-TYPE	131	70	190

Figure S509. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.001

Table S510. Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
12Q LOSS MUTATED	1	1	0	7	12	5	8
12Q LOSS WILD-TYPE	38	80	52	49	72	63	45

Figure S510. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S511. Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
12Q LOSS MUTATED	0	25	5	4
12Q LOSS WILD-TYPE	108	157	88	46

Figure S511. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S512. Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
12Q LOSS MUTATED	35	1	1	3
12Q LOSS WILD-TYPE	153	122	92	130

Figure S512. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S513. Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
12Q LOSS MUTATED	27	0	7	0	3	3	0
12Q LOSS WILD-TYPE	96	53	40	65	105	63	75

Figure S513. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S514. Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
12Q LOSS MUTATED	28	1	3	2	4
12Q LOSS WILD-TYPE	136	79	103	131	43

Figure S514. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S515. Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
12Q LOSS MUTATED	5	32	1
12Q LOSS WILD-TYPE	213	140	139

Figure S515. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0014 (Fisher's exact test), Q value = 0.0027

Table S516. Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
12Q LOSS MUTATED	19	2	5	7
12Q LOSS WILD-TYPE	97	96	87	85

Figure S516. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00031 (Fisher's exact test), Q value = 0.00065

Table S517. Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
12Q LOSS MUTATED	22	2	9
12Q LOSS WILD-TYPE	141	130	94

Figure S517. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S518. Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
13Q LOSS MUTATED	86	3	2	2
13Q LOSS WILD-TYPE	122	175	97	52

Figure S518. 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 = 2.8e-05

Table S519. Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
13Q LOSS MUTATED	47	17	17
13Q LOSS WILD-TYPE	107	61	176

Figure S519. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00016

Table S520. Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
13Q LOSS MUTATED	4	4	4	15	26	9	10
13Q LOSS WILD-TYPE	35	77	48	41	58	59	43

Figure S520. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0028

Table S521. Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
13Q LOSS MUTATED	6	40	17	9
13Q LOSS WILD-TYPE	102	142	76	41

Figure S521. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S522. Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
13Q LOSS MUTATED	61	12	6	14
13Q LOSS WILD-TYPE	127	111	87	119

Figure S522. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S523. Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
13Q LOSS MUTATED	39	4	14	0	23	12	1
13Q LOSS WILD-TYPE	84	49	33	65	85	54	74

Figure S523. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S524. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
13Q LOSS MUTATED	55	12	6	14	5
13Q LOSS WILD-TYPE	109	68	100	119	42

Figure S524. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S525. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
13Q LOSS MUTATED	30	50	12
13Q LOSS WILD-TYPE	188	122	128

Figure S525. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.06

Table S526. Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
13Q LOSS MUTATED	34	18	16	13
13Q LOSS WILD-TYPE	82	80	76	79

Figure S526. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.037

Table S527. Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
13Q LOSS MUTATED	43	18	20
13Q LOSS WILD-TYPE	120	114	83

Figure S527. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.0047

Table S528. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
14Q LOSS MUTATED	0	6	0	0
14Q LOSS WILD-TYPE	15	11	14	7

Figure S528. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0011

Table S529. Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
14Q LOSS MUTATED	1	5	0	0	0
14Q LOSS WILD-TYPE	13	4	7	7	16

Figure S529. 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 = 2.8e-05

Table S530. Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
14Q LOSS MUTATED	60	0	0	2
14Q LOSS WILD-TYPE	148	178	99	52

Figure S530. 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 = 2.8e-05

Table S531. Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
14Q LOSS MUTATED	36	12	1
14Q LOSS WILD-TYPE	118	66	192

Figure S531. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S532. Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
14Q LOSS MUTATED	1	0	4	5	20	11	9
14Q LOSS WILD-TYPE	38	81	48	51	64	57	44

Figure S532. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S533. Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
14Q LOSS MUTATED	1	33	11	5
14Q LOSS WILD-TYPE	107	149	82	45

Figure S533. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S534. Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
14Q LOSS MUTATED	53	2	3	4
14Q LOSS WILD-TYPE	135	121	90	129

Figure S534. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S535. Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
14Q LOSS MUTATED	46	1	4	0	7	4	0
14Q LOSS WILD-TYPE	77	52	43	65	101	62	75

Figure S535. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S536. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
14Q LOSS MUTATED	42	6	7	2	3
14Q LOSS WILD-TYPE	122	74	99	131	44

Figure S536. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S537. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
14Q LOSS MUTATED	12	46	2
14Q LOSS WILD-TYPE	206	126	138

Figure S537. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0013 (Fisher's exact test), Q value = 0.0025

Table S538. Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
14Q LOSS MUTATED	23	3	10	12
14Q LOSS WILD-TYPE	93	95	82	80

Figure S538. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00012

Table S539. Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
14Q LOSS MUTATED	31	4	13
14Q LOSS WILD-TYPE	132	128	90

Figure S539. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.001

Table S540. Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
15Q LOSS MUTATED	0	7	0	0
15Q LOSS WILD-TYPE	15	10	14	7

Figure S540. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S541. Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
15Q LOSS MUTATED	1	6	0	0	0
15Q LOSS WILD-TYPE	13	3	7	7	16

Figure S541. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S542. Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
15Q LOSS MUTATED	103	0	2	4
15Q LOSS WILD-TYPE	105	178	97	50

Figure S542. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S543. Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
15Q LOSS MUTATED	59	27	10
15Q LOSS WILD-TYPE	95	51	183

Figure S543. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S544. Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
15Q LOSS MUTATED	3	2	6	19	31	12	12
15Q LOSS WILD-TYPE	36	79	46	37	53	56	41

Figure S544. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S545. Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
15Q LOSS MUTATED	3	53	20	9
15Q LOSS WILD-TYPE	105	129	73	41

Figure S545. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S546. Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
15Q LOSS MUTATED	88	9	6	6
15Q LOSS WILD-TYPE	100	114	87	127

Figure S546. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S547. Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
15Q LOSS MUTATED	72	1	9	2	17	7	1
15Q LOSS WILD-TYPE	51	52	38	63	91	59	74

Figure S547. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S548. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
15Q LOSS MUTATED	79	6	4	8	10
15Q LOSS WILD-TYPE	85	74	102	125	37

Figure S548. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S549. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
15Q LOSS MUTATED	28	74	5
15Q LOSS WILD-TYPE	190	98	135

Figure S549. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S550. Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
15Q LOSS MUTATED	48	8	22	16
15Q LOSS WILD-TYPE	68	90	70	76

Figure S550. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S551. Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
15Q LOSS MUTATED	55	11	28
15Q LOSS WILD-TYPE	108	121	75

Figure S551. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'MRNA_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.0043

Table S552. Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
16P LOSS MUTATED	0	6	0	0
16P LOSS WILD-TYPE	15	11	14	7

Figure S552. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00785 (Fisher's exact test), Q value = 0.013

Table S553. Gene #69: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
16P LOSS MUTATED	2	4	0	0	0
16P LOSS WILD-TYPE	12	5	7	7	16

Figure S553. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S554. Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
16P LOSS MUTATED	94	0	3	2
16P LOSS WILD-TYPE	114	178	96	52

Figure S554. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S555. Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
16P LOSS MUTATED	51	30	8
16P LOSS WILD-TYPE	103	48	185

Figure S555. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00031

Table S556. Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
16P LOSS MUTATED	2	5	7	16	24	15	13
16P LOSS WILD-TYPE	37	76	45	40	60	53	40

Figure S556. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S557. Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
16P LOSS MUTATED	4	53	16	9
16P LOSS WILD-TYPE	104	129	77	41

Figure S557. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S558. Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
16P LOSS MUTATED	78	8	6	7
16P LOSS WILD-TYPE	110	115	87	126

Figure S558. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S559. Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
16P LOSS MUTATED	60	4	11	1	15	7	1
16P LOSS WILD-TYPE	63	49	36	64	93	59	74

Figure S559. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S560. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
16P LOSS MUTATED	67	7	5	9	8
16P LOSS WILD-TYPE	97	73	101	124	39

Figure S560. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S561. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
16P LOSS MUTATED	23	67	6
16P LOSS WILD-TYPE	195	105	134

Figure S561. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00064

Table S562. Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
16P LOSS MUTATED	38	9	19	21
16P LOSS WILD-TYPE	78	89	73	71

Figure S562. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S563. Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
16P LOSS MUTATED	48	9	30
16P LOSS WILD-TYPE	115	123	73

Figure S563. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 0.00088 (Fisher's exact test), Q value = 0.0018

Table S564. Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
16Q LOSS MUTATED	0	8	1	0
16Q LOSS WILD-TYPE	15	9	13	7

Figure S564. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00143 (Fisher's exact test), Q value = 0.0027

Table S565. Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
16Q LOSS MUTATED	2	6	0	0	1
16Q LOSS WILD-TYPE	12	3	7	7	15

Figure S565. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S566. Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
16Q LOSS MUTATED	124	3	9	4
16Q LOSS WILD-TYPE	84	175	90	50

Figure S566. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S567. Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
16Q LOSS MUTATED	71	36	16
16Q LOSS WILD-TYPE	83	42	177

Figure S567. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S568. Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
16Q LOSS MUTATED	4	7	9	20	38	16	18
16Q LOSS WILD-TYPE	35	74	43	36	46	52	35

Figure S568. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S569. Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
16Q LOSS MUTATED	10	73	18	11
16Q LOSS WILD-TYPE	98	109	75	39

Figure S569. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S570. Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
16Q LOSS MUTATED	103	14	10	13
16Q LOSS WILD-TYPE	85	109	83	120

Figure S570. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S571. Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
16Q LOSS MUTATED	79	7	16	3	22	9	4
16Q LOSS WILD-TYPE	44	46	31	62	86	57	71

Figure S571. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S572. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
16Q LOSS MUTATED	87	12	12	13	12
16Q LOSS WILD-TYPE	77	68	94	120	35

Figure S572. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S573. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
16Q LOSS MUTATED	35	89	12
16Q LOSS WILD-TYPE	183	83	128

Figure S573. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 6e-04

Table S574. Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
16Q LOSS MUTATED	49	15	27	29
16Q LOSS WILD-TYPE	67	83	65	63

Figure S574. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S575. Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
16Q LOSS MUTATED	63	18	39
16Q LOSS WILD-TYPE	100	114	64

Figure S575. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00319 (Fisher's exact test), Q value = 0.0058

Table S576. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
17P LOSS MUTATED	0	7	1	0
17P LOSS WILD-TYPE	15	10	13	7

Figure S576. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00038

Table S577. Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
17P LOSS MUTATED	1	6	1	0	0
17P LOSS WILD-TYPE	13	3	6	7	16

Figure S577. 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 = 2.8e-05

Table S578. Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
17P LOSS MUTATED	125	1	2	1
17P LOSS WILD-TYPE	83	177	97	53

Figure S578. 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 = 2.8e-05

Table S579. Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
17P LOSS MUTATED	69	31	14
17P LOSS WILD-TYPE	85	47	179

Figure S579. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S580. Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
17P LOSS MUTATED	3	2	7	20	37	14	18
17P LOSS WILD-TYPE	36	79	45	36	47	54	35

Figure S580. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S581. Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
17P LOSS MUTATED	4	68	19	10
17P LOSS WILD-TYPE	104	114	74	40

Figure S581. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S582. Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
17P LOSS MUTATED	101	5	9	13
17P LOSS WILD-TYPE	87	118	84	120

Figure S582. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S583. Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
17P LOSS MUTATED	83	1	10	3	17	13	1
17P LOSS WILD-TYPE	40	52	37	62	91	53	74

Figure S583. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S584. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
17P LOSS MUTATED	90	6	7	14	9
17P LOSS WILD-TYPE	74	74	99	119	38

Figure S584. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S585. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
17P LOSS MUTATED	29	84	13
17P LOSS WILD-TYPE	189	88	127

Figure S585. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S586. Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
17P LOSS MUTATED	50	14	25	20
17P LOSS WILD-TYPE	66	84	67	72

Figure S586. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00027 (Fisher's exact test), Q value = 0.00058

Table S587. Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
17P LOSS MUTATED	56	20	33
17P LOSS WILD-TYPE	107	112	70

Figure S587. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00248 (Fisher's exact test), Q value = 0.0046

Table S588. Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
17Q LOSS MUTATED	0	6	0	0
17Q LOSS WILD-TYPE	15	11	14	7

Figure S588. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S589. Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
17Q LOSS MUTATED	0	6	0	0	0
17Q LOSS WILD-TYPE	14	3	7	7	16

Figure S589. 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 = 2.8e-05

Table S590. Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
17Q LOSS MUTATED	90	1	1	1
17Q LOSS WILD-TYPE	118	177	98	53

Figure S590. 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 = 2.8e-05

Table S591. Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
17Q LOSS MUTATED	42	27	13
17Q LOSS WILD-TYPE	112	51	180

Figure S591. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S592. Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
17Q LOSS MUTATED	3	2	5	14	29	8	11
17Q LOSS WILD-TYPE	36	79	47	42	55	60	42

Figure S592. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S593. Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
17Q LOSS MUTATED	2	49	15	6
17Q LOSS WILD-TYPE	106	133	78	44

Figure S593. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S594. Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
17Q LOSS MUTATED	70	5	6	11
17Q LOSS WILD-TYPE	118	118	87	122

Figure S594. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S595. Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
17Q LOSS MUTATED	55	1	6	3	15	12	0
17Q LOSS WILD-TYPE	68	52	41	62	93	54	75

Figure S595. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S596. Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
17Q LOSS MUTATED	59	6	6	12	7
17Q LOSS WILD-TYPE	105	74	100	121	40

Figure S596. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S597. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
17Q LOSS MUTATED	25	54	11
17Q LOSS WILD-TYPE	193	118	129

Figure S597. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00552 (Fisher's exact test), Q value = 0.0096

Table S598. Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
17Q LOSS MUTATED	36	12	16	16
17Q LOSS WILD-TYPE	80	86	76	76

Figure S598. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.034

Table S599. Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
17Q LOSS MUTATED	43	18	19
17Q LOSS WILD-TYPE	120	114	84

Figure S599. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S600. Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
18P LOSS MUTATED	49	0	1	1
18P LOSS WILD-TYPE	159	178	98	53

Figure S600. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S601. Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
18P LOSS MUTATED	29	11	5
18P LOSS WILD-TYPE	125	67	188

Figure S601. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.042

Table S602. Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
18P LOSS MUTATED	3	3	6	4	16	4	8
18P LOSS WILD-TYPE	36	78	46	52	68	64	45

Figure S602. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.002

Table S603. Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
18P LOSS MUTATED	2	28	10	4
18P LOSS WILD-TYPE	106	154	83	46

Figure S603. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S604. Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
18P LOSS MUTATED	35	6	4	6
18P LOSS WILD-TYPE	153	117	89	127

Figure S604. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S605. Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
18P LOSS MUTATED	21	1	6	1	16	6	0
18P LOSS WILD-TYPE	102	52	41	64	92	60	75

Figure S605. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S606. Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
18P LOSS MUTATED	32	6	1	7	4
18P LOSS WILD-TYPE	132	74	105	126	43

Figure S606. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.0058

Table S607. Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
18P LOSS MUTATED	20	25	5
18P LOSS WILD-TYPE	198	147	135

Figure S607. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00897 (Fisher's exact test), Q value = 0.015

Table S608. Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
18P LOSS MUTATED	22	5	7	11
18P LOSS WILD-TYPE	94	93	85	81

Figure S608. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.018

Table S609. Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
18P LOSS MUTATED	28	10	7
18P LOSS WILD-TYPE	135	122	96

Figure S609. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S610. Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
18Q LOSS MUTATED	61	0	1	1
18Q LOSS WILD-TYPE	147	178	98	53

Figure S610. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S611. Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
18Q LOSS MUTATED	35	14	7
18Q LOSS WILD-TYPE	119	64	186

Figure S611. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.017

Table S612. Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
18Q LOSS MUTATED	5	3	5	9	20	7	6
18Q LOSS WILD-TYPE	34	78	47	47	64	61	47

Figure S612. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0019

Table S613. Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
18Q LOSS MUTATED	5	35	12	3
18Q LOSS WILD-TYPE	103	147	81	47

Figure S613. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S614. Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
18Q LOSS MUTATED	42	7	7	7
18Q LOSS WILD-TYPE	146	116	86	126

Figure S614. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S615. Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
18Q LOSS MUTATED	26	1	12	1	18	5	0
18Q LOSS WILD-TYPE	97	52	35	64	90	61	75

Figure S615. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S616. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
18Q LOSS MUTATED	38	6	3	9	6
18Q LOSS WILD-TYPE	126	74	103	124	41

Figure S616. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S617. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
18Q LOSS MUTATED	20	36	6
18Q LOSS WILD-TYPE	198	136	134

Figure S617. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.018

Table S618. Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
18Q LOSS MUTATED	26	7	10	13
18Q LOSS WILD-TYPE	90	91	82	79

Figure S618. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.018

Table S619. Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
18Q LOSS MUTATED	33	11	12
18Q LOSS WILD-TYPE	130	121	91

Figure S619. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S620. Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
19P LOSS MUTATED	55	0	0	2
19P LOSS WILD-TYPE	153	178	99	52

Figure S620. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S621. Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
19P LOSS MUTATED	42	8	2
19P LOSS WILD-TYPE	112	70	191

Figure S621. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00029

Table S622. Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
19P LOSS MUTATED	1	0	7	9	16	8	7
19P LOSS WILD-TYPE	38	81	45	47	68	60	46

Figure S622. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00027

Table S623. Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
19P LOSS MUTATED	2	31	12	3
19P LOSS WILD-TYPE	106	151	81	47

Figure S623. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S624. Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
19P LOSS MUTATED	44	4	5	4
19P LOSS WILD-TYPE	144	119	88	129

Figure S624. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S625. Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
19P LOSS MUTATED	34	1	8	1	10	3	0
19P LOSS WILD-TYPE	89	52	39	64	98	63	75

Figure S625. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S626. Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
19P LOSS MUTATED	42	3	2	5	4
19P LOSS WILD-TYPE	122	77	104	128	43

Figure S626. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S627. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
19P LOSS MUTATED	15	38	3
19P LOSS WILD-TYPE	203	134	137

Figure S627. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00385 (Fisher's exact test), Q value = 0.0069

Table S628. Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
19P LOSS MUTATED	24	5	8	13
19P LOSS WILD-TYPE	92	93	84	79

Figure S628. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S629. Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
19P LOSS MUTATED	36	4	10
19P LOSS WILD-TYPE	127	128	93

Figure S629. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S630. Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
19Q LOSS MUTATED	51	0	1	2
19Q LOSS WILD-TYPE	157	178	98	52

Figure S630. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S631. Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
19Q LOSS MUTATED	32	12	4
19Q LOSS WILD-TYPE	122	66	189

Figure S631. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S632. Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
19Q LOSS MUTATED	1	0	5	6	20	6	7
19Q LOSS WILD-TYPE	38	81	47	50	64	62	46

Figure S632. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00021

Table S633. Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
19Q LOSS MUTATED	2	31	10	2
19Q LOSS WILD-TYPE	106	151	83	48

Figure S633. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S634. Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
19Q LOSS MUTATED	39	4	5	5
19Q LOSS WILD-TYPE	149	119	88	128

Figure S634. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S635. Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
19Q LOSS MUTATED	34	1	5	1	8	4	0
19Q LOSS WILD-TYPE	89	52	42	64	100	62	75

Figure S635. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S636. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
19Q LOSS MUTATED	37	3	3	6	4
19Q LOSS WILD-TYPE	127	77	103	127	43

Figure S636. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 9.8e-05

Table S637. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
19Q LOSS MUTATED	16	33	4
19Q LOSS WILD-TYPE	202	139	136

Figure S637. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00601 (Fisher's exact test), Q value = 0.01

Table S638. Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
19Q LOSS MUTATED	24	6	8	8
19Q LOSS WILD-TYPE	92	92	84	84

Figure S638. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00077

Table S639. Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
19Q LOSS MUTATED	30	5	11
19Q LOSS WILD-TYPE	133	127	92

Figure S639. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S640. Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
20P LOSS MUTATED	20	0	1	1
20P LOSS WILD-TYPE	188	178	98	53

Figure S640. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.062

Table S641. Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
20P LOSS MUTATED	1	13	2	1
20P LOSS WILD-TYPE	107	169	91	49

Figure S641. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0242 (Fisher's exact test), Q value = 0.038

Table S642. Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
20P LOSS MUTATED	14	2	3	2
20P LOSS WILD-TYPE	174	121	90	131

Figure S642. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.019

Table S643. Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
20P LOSS MUTATED	11	2	3	0	4	1	0
20P LOSS WILD-TYPE	112	51	44	65	104	65	75

Figure S643. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.017

Table S644. Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
20P LOSS MUTATED	5	13	2
20P LOSS WILD-TYPE	213	159	138

Figure S644. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 0.00187 (Fisher's exact test), Q value = 0.0035

Table S645. Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
20Q LOSS MUTATED	10	0	0	1
20Q LOSS WILD-TYPE	198	178	99	53

Figure S645. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.026

Table S646. Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
20Q LOSS MUTATED	4	3	0
20Q LOSS WILD-TYPE	150	75	193

Figure S646. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'RPPA_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.051

Table S647. Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
20Q LOSS MUTATED	2	0	0	4	3	1	0
20Q LOSS WILD-TYPE	37	81	52	52	81	67	53

Figure S647. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00545 (Fisher's exact test), Q value = 0.0095

Table S648. Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
20Q LOSS MUTATED	2	8	0
20Q LOSS WILD-TYPE	216	164	140

Figure S648. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.053

Table S649. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
21Q LOSS MUTATED	0	4	0	0
21Q LOSS WILD-TYPE	15	13	14	7

Figure S649. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.044

Table S650. Gene #79: '21q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
21Q LOSS MUTATED	1	3	0	0	0
21Q LOSS WILD-TYPE	13	6	7	7	16

Figure S650. 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 = 2.8e-05

Table S651. Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
21Q LOSS MUTATED	47	2	2	3
21Q LOSS WILD-TYPE	161	176	97	51

Figure S651. 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 = 2.8e-05

Table S652. Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
21Q LOSS MUTATED	31	10	5
21Q LOSS WILD-TYPE	123	68	188

Figure S652. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'RPPA_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.027

Table S653. Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
21Q LOSS MUTATED	2	3	4	6	18	6	6
21Q LOSS WILD-TYPE	37	78	48	50	66	62	47

Figure S653. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0025

Table S654. Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
21Q LOSS MUTATED	3	30	8	4
21Q LOSS WILD-TYPE	105	152	85	46

Figure S654. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S655. Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
21Q LOSS MUTATED	42	3	8	1
21Q LOSS WILD-TYPE	146	120	85	132

Figure S655. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S656. Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
21Q LOSS MUTATED	30	1	7	4	10	2	0
21Q LOSS WILD-TYPE	93	52	40	61	98	64	75

Figure S656. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S657. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
21Q LOSS MUTATED	38	5	6	1	2
21Q LOSS WILD-TYPE	126	75	100	132	45

Figure S657. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S658. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
21Q LOSS MUTATED	15	36	1
21Q LOSS WILD-TYPE	203	136	139

Figure S658. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S659. Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
21Q LOSS MUTATED	21	0	9	16
21Q LOSS WILD-TYPE	95	98	83	76

Figure S659. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S660. Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
21Q LOSS MUTATED	31	3	12
21Q LOSS WILD-TYPE	132	129	91

Figure S660. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.0048

Table S661. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
22Q LOSS MUTATED	0	6	0	0
22Q LOSS WILD-TYPE	15	11	14	7

Figure S661. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.012

Table S662. Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
22Q LOSS MUTATED	2	4	0	0	0
22Q LOSS WILD-TYPE	12	5	7	7	16

Figure S662. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S663. Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
22Q LOSS MUTATED	106	1	2	1
22Q LOSS WILD-TYPE	102	177	97	53

Figure S663. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S664. Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
22Q LOSS MUTATED	58	27	16
22Q LOSS WILD-TYPE	96	51	177

Figure S664. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S665. Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
22Q LOSS MUTATED	3	3	7	19	29	9	15
22Q LOSS WILD-TYPE	36	78	45	37	55	59	38

Figure S665. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S666. Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
22Q LOSS MUTATED	3	50	21	11
22Q LOSS WILD-TYPE	105	132	72	39

Figure S666. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S667. Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
22Q LOSS MUTATED	81	7	6	15
22Q LOSS WILD-TYPE	107	116	87	118

Figure S667. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S668. Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
22Q LOSS MUTATED	63	1	7	1	22	13	2
22Q LOSS WILD-TYPE	60	52	40	64	86	53	73

Figure S668. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S669. Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
22Q LOSS MUTATED	76	6	2	16	8
22Q LOSS WILD-TYPE	88	74	104	117	39

Figure S669. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S670. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
22Q LOSS MUTATED	29	66	13
22Q LOSS WILD-TYPE	189	106	127

Figure S670. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.016

Table S671. Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
22Q LOSS MUTATED	40	16	22	17
22Q LOSS WILD-TYPE	76	82	70	75

Figure S671. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00122 (Fisher's exact test), Q value = 0.0024

Table S672. Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
22Q LOSS MUTATED	51	18	26
22Q LOSS WILD-TYPE	112	114	77

Figure S672. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00059 (Fisher's exact test), Q value = 0.0012

Table S673. Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
XP LOSS MUTATED	0	7	0	0
XP LOSS WILD-TYPE	15	10	14	7

Figure S673. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.0018

Table S674. Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
XP LOSS MUTATED	2	5	0	0	0
XP LOSS WILD-TYPE	12	4	7	7	16

Figure S674. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S675. Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
XP LOSS MUTATED	84	1	0	1
XP LOSS WILD-TYPE	124	177	99	53

Figure S675. 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 = 2.8e-05

Table S676. Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
XP LOSS MUTATED	37	25	9
XP LOSS WILD-TYPE	117	53	184

Figure S676. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S677. Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
XP LOSS MUTATED	3	2	7	14	30	6	10
XP LOSS WILD-TYPE	36	79	45	42	54	62	43

Figure S677. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S678. Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
XP LOSS MUTATED	3	54	11	4
XP LOSS WILD-TYPE	105	128	82	46

Figure S678. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S679. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
XP LOSS MUTATED	68	7	5	5
XP LOSS WILD-TYPE	120	116	88	128

Figure S679. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S680. Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
XP LOSS MUTATED	53	2	6	1	19	4	0
XP LOSS WILD-TYPE	70	51	41	64	89	62	75

Figure S680. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S681. Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
XP LOSS MUTATED	57	6	7	8	5
XP LOSS WILD-TYPE	107	74	99	125	42

Figure S681. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S682. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
XP LOSS MUTATED	22	57	4
XP LOSS WILD-TYPE	196	115	136

Figure S682. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S683. Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
XP LOSS MUTATED	38	9	12	11
XP LOSS WILD-TYPE	78	89	80	81

Figure S683. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 7.5e-05

Table S684. Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
XP LOSS MUTATED	42	8	20
XP LOSS WILD-TYPE	121	124	83

Figure S684. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.00247 (Fisher's exact test), Q value = 0.0046

Table S685. Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	15	17	14	7
XQ LOSS MUTATED	0	6	0	0
XQ LOSS WILD-TYPE	15	11	14	7

Figure S685. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00752 (Fisher's exact test), Q value = 0.013

Table S686. Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
XQ LOSS MUTATED	2	4	0	0	0
XQ LOSS WILD-TYPE	12	5	7	7	16

Figure S686. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S687. Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	208	178	99	54
XQ LOSS MUTATED	67	1	0	2
XQ LOSS WILD-TYPE	141	177	99	52

Figure S687. 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 = 2.8e-05

Table S688. Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	154	78	193
XQ LOSS MUTATED	33	20	6
XQ LOSS WILD-TYPE	121	58	187

Figure S688. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.3e-05

Table S689. Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	39	81	52	56	84	68	53
XQ LOSS MUTATED	3	1	6	13	22	6	7
XQ LOSS WILD-TYPE	36	80	46	43	62	62	46

Figure S689. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S690. Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	108	182	93	50
XQ LOSS MUTATED	2	45	7	4
XQ LOSS WILD-TYPE	106	137	86	46

Figure S690. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S691. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	188	123	93	133
XQ LOSS MUTATED	55	5	5	4
XQ LOSS WILD-TYPE	133	118	88	129

Figure S691. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S692. Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	123	53	47	65	108	66	75
XQ LOSS MUTATED	40	2	7	1	15	4	0
XQ LOSS WILD-TYPE	83	51	40	64	93	62	75

Figure S692. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S693. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	164	80	106	133	47
XQ LOSS MUTATED	47	5	5	7	3
XQ LOSS WILD-TYPE	117	75	101	126	44

Figure S693. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S694. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	218	172	140
XQ LOSS MUTATED	17	46	4
XQ LOSS WILD-TYPE	201	126	136

Figure S694. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.0052

Table S695. Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	116	98	92	92
XQ LOSS MUTATED	28	8	8	14
XQ LOSS WILD-TYPE	88	90	84	78

Figure S695. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.8e-05

Table S696. Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	163	132	103
XQ LOSS MUTATED	38	5	15
XQ LOSS WILD-TYPE	125	127	88

Figure S696. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #12: '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/UCEC-TP/22534123/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/22553827/UCEC-TP.transferedmergedcluster.txt
Number of patients = 539
Number of significantly arm-level cnvs = 82
Number of molecular subtypes = 12
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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