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, 622 significant findings detected with P value < 0.05 and Q value < 0.25.

1p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_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_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
2p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4p gain cnv correlated to 'CN_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
4q gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
5p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
5q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
7p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.
7q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
8p gain cnv correlated to 'CN_CNMF', 'RPPA_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.
8q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
9q gain cnv correlated to 'CN_CNMF'.
10p gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q gain cnv correlated to 'MRNA_CNMF', 'CN_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
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', 'RPPA_CHIERARCHICAL', and 'MRNASEQ_CNMF'.
12p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
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', and 'MIRSEQ_CNMF'.
16q gain cnv correlated to 'CN_CNMF'.
17p gain cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
17q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
18p gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q gain cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
19q 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'.
20p gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20q gain cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
21q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
22q gain cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
xp gain cnv correlated to 'CN_CNMF'.
xq gain cnv correlated to 'CN_CNMF'.
1p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
1q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
2p loss cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
2q loss cnv correlated to 'CN_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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
3q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.
4p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
4q 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'.
5p 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'.
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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
6q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
7p loss cnv correlated to 'MRNA_CNMF', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
9q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10p loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
10q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
11q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', '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_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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 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', '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', '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', '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', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
17q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
18q loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19p loss cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
19q loss cnv correlated to 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
20p loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.
20q loss cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
21q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
22q loss cnv correlated to 'MRNA_CNMF', 'MRNA_CHIERARCHICAL', 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CNMF', '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', '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', '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, 622 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
8q gain	159 (29%)	380	0.0104 (0.0191)	0.031 (0.0524)	1e-05 (2.95e-05)	0.04 (0.065)	0.0003 (0.000725)	0.0219 (0.0382)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00019 (0.000476)	1e-05 (2.95e-05)	0.00046 (0.00107)	0.00745 (0.0142)
5q loss	74 (14%)	465	0.0132 (0.0238)	0.00999 (0.0185)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0012 (0.00261)	0.00246 (0.00511)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00014 (0.000355)	3e-05 (8.22e-05)
8p loss	80 (15%)	459	0.00782 (0.0147)	4e-05 (0.000108)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0335 (0.0561)	0.0251 (0.0433)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
14q loss	61 (11%)	478	0.0021 (0.00443)	0.00045 (0.00105)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0143 (0.0256)	0.0499 (0.079)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00497 (0.00972)	2e-05 (5.64e-05)
20q gain	132 (24%)	407	0.00198 (0.00421)	0.00711 (0.0135)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0321 (0.054)	0.673 (0.779)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
3p loss	51 (9%)	488	0.0383 (0.063)	0.00073 (0.00164)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0225 (0.0391)	0.125 (0.18)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0151 (0.027)	0.0001 (0.000258)
4p loss	105 (19%)	434	0.0037 (0.00748)	0.00163 (0.00349)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00106 (0.00233)	0.188 (0.259)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
9p loss	103 (19%)	436	0.00114 (0.00249)	2e-05 (5.64e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00379 (0.00761)	0.562 (0.669)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0091 (0.017)	0.00062 (0.0014)
9q loss	122 (23%)	417	4e-05 (0.000108)	3e-05 (8.22e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00037 (0.000884)	0.7 (0.806)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00111 (0.00243)	5e-05 (0.000133)
15q loss	109 (20%)	430	0.00074 (0.00165)	7e-05 (0.000184)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0009 (0.002)	0.484 (0.589)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	2e-05 (5.64e-05)	1e-05 (2.95e-05)
17p loss	130 (24%)	409	0.00328 (0.00672)	0.00014 (0.000355)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00361 (0.00732)	0.369 (0.463)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
22q loss	109 (20%)	430	0.00196 (0.00417)	0.00759 (0.0144)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0388 (0.0638)	0.279 (0.365)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00382 (0.00766)	0.00013 (0.000332)
xp loss	85 (16%)	454	0.00164 (0.00351)	0.0004 (0.000946)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	2e-05 (5.64e-05)	0.219 (0.295)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00066 (0.00149)	1e-05 (2.95e-05)
xq loss	71 (13%)	468	0.00831 (0.0156)	0.0047 (0.00923)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0002 (0.000498)	0.214 (0.29)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00576 (0.0111)	1e-05 (2.95e-05)
13q gain	30 (6%)	509	0.138 (0.197)	0.0068 (0.013)	1e-05 (2.95e-05)	6e-05 (0.000158)	0.252 (0.334)	0.0116 (0.0213)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00707 (0.0135)	0.0236 (0.041)
20p gain	112 (21%)	427	0.00803 (0.0151)	0.0494 (0.0783)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.163 (0.23)	0.743 (0.849)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00025 (0.000613)	1e-05 (2.95e-05)
4q loss	105 (19%)	434	0.151 (0.214)	0.00513 (0.01)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0135 (0.0243)	0.19 (0.262)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
5p loss	55 (10%)	484	0.0517 (0.0811)	0.0394 (0.0642)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00378 (0.00761)	0.104 (0.153)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	5e-05 (0.000133)	0.00086 (0.00191)
7q loss	42 (8%)	497			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0462 (0.0736)	0.014 (0.0251)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00266 (0.00549)	0.00034 (0.000816)
10p loss	43 (8%)	496	0.039 (0.0639)	0.0295 (0.0504)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0551 (0.0859)	0.187 (0.259)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0251 (0.0433)	0.00406 (0.00809)
12p loss	43 (8%)	496	0.138 (0.197)	0.165 (0.232)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0416 (0.067)	0.0376 (0.0622)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00038 (0.000905)	0.0025 (0.00518)
16p loss	97 (18%)	442	0.00232 (0.00485)	0.00767 (0.0145)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.092 (0.138)	0.321 (0.412)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00416 (0.00825)	1e-05 (2.95e-05)
16q loss	138 (26%)	401	0.0008 (0.00179)	0.00135 (0.00292)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.345 (0.439)	0.974 (1.00)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00026 (0.000636)	1e-05 (2.95e-05)
17q loss	93 (17%)	446	0.00199 (0.00422)	2e-05 (5.64e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.107 (0.157)	0.919 (1.00)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00417 (0.00826)	0.00052 (0.0012)
21q loss	54 (10%)	485	0.0401 (0.065)	0.0299 (0.051)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.24 (0.321)	0.425 (0.524)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00364 (0.00737)	2e-05 (5.64e-05)
1p gain	50 (9%)	489	0.535 (0.643)	0.218 (0.295)	1e-05 (2.95e-05)	0.00046 (0.00107)	0.0453 (0.0723)	0.263 (0.347)	1e-05 (2.95e-05)	3e-05 (8.22e-05)	2e-05 (5.64e-05)	4e-05 (0.000108)	0.00239 (0.00498)	0.00294 (0.00605)
18p gain	72 (13%)	467	0.335 (0.429)	0.241 (0.321)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0121 (0.022)	0.163 (0.231)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
18q gain	45 (8%)	494	0.255 (0.337)	0.0432 (0.0693)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.279 (0.365)	0.0953 (0.142)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	2e-05 (5.64e-05)	0.0001 (0.000258)
19p gain	54 (10%)	485	0.0393 (0.0641)	0.0302 (0.0513)	1e-05 (2.95e-05)	0.00027 (0.000659)	0.908 (0.997)	0.0752 (0.115)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0004 (0.000946)	0.0826 (0.125)
19q gain	57 (11%)	482			1e-05 (2.95e-05)	3e-05 (8.22e-05)	0.487 (0.592)	0.0431 (0.0692)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00021 (0.00052)	0.0136 (0.0244)
3q loss	31 (6%)	508	0.0382 (0.0629)	0.00072 (0.00162)	1e-05 (2.95e-05)	5e-05 (0.000133)	0.0642 (0.0988)	0.263 (0.347)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00018 (0.000452)	0.0124 (0.0226)	0.0968 (0.144)
6q loss	25 (5%)	514	0.377 (0.471)	0.0301 (0.0513)	1e-05 (2.95e-05)	3e-05 (8.22e-05)	0.478 (0.583)	0.804 (0.91)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00018 (0.000452)	2e-05 (5.64e-05)	0.0124 (0.0226)	0.00358 (0.00729)
12q loss	36 (7%)	503			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.102 (0.151)	0.0156 (0.0277)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	3e-05 (8.22e-05)	0.00045 (0.00105)
19q loss	56 (10%)	483	0.255 (0.337)	0.0167 (0.0296)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.25 (0.333)	0.717 (0.823)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0117 (0.0214)	2e-05 (5.64e-05)
2p gain	95 (18%)	444	0.857 (0.956)	0.372 (0.466)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0567 (0.0881)	0.244 (0.325)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	6e-05 (0.000158)	0.00017 (0.000429)
2q gain	79 (15%)	460	0.343 (0.437)	0.602 (0.71)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0635 (0.0979)	0.132 (0.191)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	9e-05 (0.000234)	0.0003 (0.000725)
3p gain	49 (9%)	490			1e-05 (2.95e-05)	0.00926 (0.0172)	0.302 (0.391)	0.947 (1.00)	4e-05 (0.000108)	0.00554 (0.0107)	0.00111 (0.00243)	0.00099 (0.00219)	0.0149 (0.0266)	0.0357 (0.0595)
3q gain	84 (16%)	455	0.617 (0.727)	0.253 (0.335)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.105 (0.155)	0.16 (0.227)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00028 (0.00068)	5e-05 (0.000133)
5p gain	51 (9%)	488	1 (1.00)	0.514 (0.622)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.147 (0.21)	0.705 (0.81)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00021 (0.00052)	1e-05 (2.95e-05)
6p gain	80 (15%)	459	0.208 (0.284)	0.664 (0.771)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0984 (0.146)	0.833 (0.94)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00211 (0.00445)	0.0194 (0.0339)
12p gain	71 (13%)	468	0.387 (0.48)	0.688 (0.795)	1e-05 (2.95e-05)	3e-05 (8.22e-05)	0.915 (1.00)	0.972 (1.00)	1e-05 (2.95e-05)	4e-05 (0.000108)	0.00056 (0.00128)	0.00062 (0.0014)	0.00402 (0.00802)	0.00346 (0.00706)
22q gain	31 (6%)	508			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.372 (0.466)	0.187 (0.259)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	4e-05 (0.000108)	2e-05 (5.64e-05)
6p loss	18 (3%)	521	0.376 (0.47)	0.029 (0.0498)	1e-05 (2.95e-05)	0.00127 (0.00276)	0.364 (0.458)	1 (1.00)	0.00037 (0.000884)	0.0002 (0.000498)	0.00627 (0.0121)	0.00397 (0.00794)	0.0696 (0.107)	0.0247 (0.0427)
7p loss	44 (8%)	495	0.0399 (0.0648)	0.193 (0.266)	1e-05 (2.95e-05)	0.0004 (0.000946)	0.0371 (0.0614)	0.553 (0.661)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.062 (0.096)	0.0619 (0.0959)
8q loss	25 (5%)	514			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.327 (0.42)	0.837 (0.944)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	3e-05 (8.22e-05)	1e-05 (2.95e-05)	0.00095 (0.00211)	0.0087 (0.0163)
10q loss	40 (7%)	499	0.136 (0.195)	0.167 (0.235)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0546 (0.0852)	0.17 (0.239)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0316 (0.0531)	0.00466 (0.00917)
11p loss	75 (14%)	464			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.3 (0.39)	0.331 (0.424)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00046 (0.00107)	2e-05 (5.64e-05)
11q loss	72 (13%)	467			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.852 (0.954)	0.789 (0.897)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)
13q loss	93 (17%)	446	0.905 (0.996)	0.196 (0.269)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0245 (0.0425)	0.5 (0.607)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	2e-05 (5.64e-05)	1e-05 (2.95e-05)	0.165 (0.232)	0.00203 (0.0043)
18p loss	52 (10%)	487			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.477 (0.583)	0.567 (0.674)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0001 (0.000258)	8e-05 (0.000208)	0.0174 (0.0306)	0.00361 (0.00732)
18q loss	65 (12%)	474	0.535 (0.643)	0.514 (0.622)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.531 (0.639)	1 (1.00)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0115 (0.0211)	0.00041 (0.000967)
19p loss	59 (11%)	480			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.097 (0.144)	0.27 (0.354)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00523 (0.0102)	1e-05 (2.95e-05)
1q gain	188 (35%)	351	0.182 (0.253)	0.0102 (0.0188)	1e-05 (2.95e-05)	0.187 (0.259)	0.0935 (0.14)	0.0157 (0.028)	2e-05 (5.64e-05)	0.00017 (0.000429)	1e-05 (2.95e-05)	0.017 (0.03)	0.901 (0.995)	0.077 (0.118)
5q gain	20 (4%)	519			1e-05 (2.95e-05)	0.0357 (0.0595)	0.368 (0.463)	0.29 (0.377)	0.00025 (0.000613)	0.00652 (0.0125)	0.00251 (0.00519)	0.00014 (0.000355)	0.23 (0.308)	0.00012 (0.000307)
6q gain	64 (12%)	475	0.207 (0.283)	0.661 (0.771)	1e-05 (2.95e-05)	0.00045 (0.00105)	0.0515 (0.0809)	0.758 (0.865)	2e-05 (5.64e-05)	0.00049 (0.00113)	0.001 (0.00221)	5e-05 (0.000133)	0.0159 (0.0283)	0.303 (0.392)
11p gain	23 (4%)	516	0.0392 (0.0641)	0.197 (0.27)	1e-05 (2.95e-05)	0.0444 (0.071)	0.055 (0.0857)	0.114 (0.166)	0.00327 (0.00672)	0.00149 (0.00322)	0.00223 (0.00467)	0.00672 (0.0129)	0.228 (0.307)	0.362 (0.457)
17q gain	30 (6%)	509			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.0412 (0.0665)	1 (1.00)	3e-05 (8.22e-05)	1e-05 (2.95e-05)	0.00012 (0.000307)	0.0022 (0.00462)	0.05 (0.079)	0.0915 (0.137)
21q gain	39 (7%)	500			1e-05 (2.95e-05)	0.00046 (0.00107)	0.425 (0.524)	0.454 (0.556)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.00034 (0.000816)	0.234 (0.313)
1p loss	25 (5%)	514			1e-05 (2.95e-05)	1e-05 (2.95e-05)	0.787 (0.897)	0.362 (0.457)	1e-05 (2.95e-05)	1e-05 (2.95e-05)	8e-05 (0.000208)	1e-05 (2.95e-05)	0.29 (0.377)	0.0006 (0.00136)
1q loss	14 (3%)	525			1e-05 (2.95e-05)	3e-05 (8.22e-05)			8e-05 (0.000208)	0.00108 (0.00237)	0.00032 (0.000772)	1e-05 (2.95e-05)	0.526 (0.634)	0.0075 (0.0142)
4p gain	14 (3%)	525			1e-05 (2.95e-05)	0.846 (0.95)	0.374 (0.467)	0.0379 (0.0625)	0.00055 (0.00126)	0.0452 (0.0722)	0.00407 (0.00809)	0.00055 (0.00126)	0.348 (0.441)	0.435 (0.533)
14q gain	37 (7%)	502	1 (1.00)	0.843 (0.948)	1e-05 (2.95e-05)	0.00215 (0.00452)	0.0859 (0.13)	0.691 (0.796)	0.00023 (0.000569)	0.00062 (0.0014)	0.0062 (0.012)	0.00049 (0.00113)	0.0926 (0.139)	0.312 (0.402)
7p gain	67 (12%)	472	0.853 (0.954)	0.905 (0.996)	1e-05 (2.95e-05)	0.00134 (0.0029)	0.846 (0.95)	0.864 (0.963)	0.039 (0.0639)	0.0624 (0.0963)	0.0132 (0.0238)	0.431 (0.53)	0.0311 (0.0525)	0.0528 (0.0826)
9p gain	22 (4%)	517			7e-05 (0.000184)	0.00379 (0.00761)	0.0957 (0.142)	0.327 (0.42)	0.00501 (0.00978)	0.0132 (0.0239)	0.0107 (0.0197)	0.111 (0.162)	0.105 (0.155)	0.369 (0.463)
12q gain	54 (10%)	485	0.386 (0.48)	0.687 (0.794)	1e-05 (2.95e-05)	0.0088 (0.0164)	0.963 (1.00)	0.981 (1.00)	0.00439 (0.00867)	0.0422 (0.0678)	0.0486 (0.0771)	0.107 (0.157)	0.2 (0.274)	0.275 (0.36)
2q loss	17 (3%)	522			2e-05 (5.64e-05)	0.116 (0.167)			0.00028 (0.00068)	0.0146 (0.0262)	0.0185 (0.0324)	0.0302 (0.0513)	0.416 (0.515)	0.801 (0.908)
20q loss	9 (2%)	530			0.0005 (0.00115)	0.0864 (0.131)	0.644 (0.752)	1 (1.00)	0.037 (0.0614)	0.0307 (0.052)	0.0405 (0.0655)	0.047 (0.0747)	0.174 (0.243)	0.251 (0.333)
8p gain	118 (22%)	421	0.356 (0.451)	0.402 (0.498)	1e-05 (2.95e-05)	0.883 (0.978)	0.0214 (0.0373)	0.217 (0.294)	0.139 (0.199)	0.0358 (0.0596)	0.307 (0.396)	0.0291 (0.05)	0.116 (0.167)	0.508 (0.616)
10p gain	117 (22%)	422	0.0077 (0.0145)	0.09 (0.136)	1e-05 (2.95e-05)	0.872 (0.969)	0.193 (0.266)	0.814 (0.921)	0.0932 (0.139)	0.165 (0.232)	0.575 (0.682)	0.0185 (0.0325)	0.537 (0.644)	0.0359 (0.0597)
16p gain	27 (5%)	512			1e-05 (2.95e-05)	0.00245 (0.0051)	0.18 (0.25)	0.634 (0.745)	0.019 (0.0333)	0.0523 (0.082)	0.00337 (0.00689)	0.237 (0.317)	0.145 (0.207)	0.358 (0.454)
20p loss	19 (4%)	520			1e-05 (2.95e-05)	0.21 (0.286)	0.465 (0.569)	0.665 (0.771)	0.0162 (0.0286)	0.0103 (0.019)	0.00707 (0.0135)	0.0513 (0.0808)	0.421 (0.52)	0.43 (0.529)
7q gain	66 (12%)	473	0.854 (0.954)	0.903 (0.996)	1e-05 (2.95e-05)	0.00151 (0.00324)	0.854 (0.954)	0.537 (0.644)	0.178 (0.248)	0.0274 (0.0471)	0.0817 (0.124)	0.476 (0.582)	0.0898 (0.136)	0.209 (0.285)
10q gain	109 (20%)	430	0.00495 (0.0097)	0.0914 (0.137)	4e-05 (0.000108)	0.727 (0.832)	0.123 (0.178)	0.662 (0.771)	0.14 (0.2)	0.379 (0.472)	0.34 (0.434)	0.00195 (0.00416)	0.565 (0.671)	0.0603 (0.0936)
11q gain	19 (4%)	520			1e-05 (2.95e-05)	0.115 (0.166)	0.179 (0.249)	0.0115 (0.0211)	0.0333 (0.0559)	0.102 (0.151)	0.209 (0.285)	0.0913 (0.137)	0.885 (0.979)	0.652 (0.761)
4q gain	8 (1%)	531			0.00457 (0.00901)	0.618 (0.727)			0.0293 (0.0502)	0.547 (0.655)	0.271 (0.356)	0.0757 (0.116)	0.796 (0.904)	0.635 (0.745)
17p gain	12 (2%)	527			0.0015 (0.00323)	0.16 (0.227)	0.224 (0.302)	1 (1.00)	0.114 (0.166)	0.0413 (0.0666)	0.0774 (0.118)	0.134 (0.193)	0.347 (0.441)	0.665 (0.771)
2p loss	11 (2%)	528			0.00024 (0.000592)	0.301 (0.39)			0.00533 (0.0103)	0.0808 (0.123)	0.401 (0.497)	0.107 (0.157)	0.559 (0.667)	0.721 (0.826)
9q gain	9 (2%)	530			0.0308 (0.0521)	0.167 (0.235)			0.36 (0.455)	0.305 (0.394)	0.171 (0.24)	0.511 (0.62)	0.663 (0.771)	0.263 (0.347)
15q gain	11 (2%)	528			0.00057 (0.0013)	0.915 (1.00)			0.691 (0.796)	0.591 (0.699)	0.638 (0.747)	0.913 (1.00)	1 (1.00)	0.249 (0.332)
16q gain	10 (2%)	529			0.0121 (0.022)	0.0511 (0.0805)	0.944 (1.00)	0.839 (0.945)	0.111 (0.162)	0.284 (0.37)	0.0707 (0.109)	0.211 (0.287)	0.623 (0.732)	0.796 (0.904)
xp gain	64 (12%)	475	0.576 (0.682)	0.908 (0.997)	1e-05 (2.95e-05)	0.108 (0.158)	0.874 (0.969)	0.558 (0.665)	0.525 (0.634)	0.788 (0.897)	0.266 (0.349)	0.818 (0.924)	0.227 (0.306)	0.425 (0.524)
xq gain	64 (12%)	475	0.705 (0.81)	0.927 (1.00)	1e-05 (2.95e-05)	0.587 (0.694)	0.874 (0.969)	0.337 (0.431)	0.639 (0.747)	0.885 (0.979)	0.555 (0.663)	0.981 (1.00)	0.224 (0.302)	0.87 (0.969)

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1P GAIN MUTATED	38	6	2	0	4
1P GAIN WILD-TYPE	131	299	17	9	33

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
1P GAIN MUTATED	30	5	10
1P GAIN WILD-TYPE	135	84	161

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

'1p gain' versus 'RPPA_CNMF'

P value = 0.0453 (Fisher's exact test), Q value = 0.072

Table S3. Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
1P GAIN MUTATED	2	6	0	1	1	2
1P GAIN WILD-TYPE	39	31	39	11	40	22

Figure S3. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S4. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
1P GAIN MUTATED	39	6	5
1P GAIN WILD-TYPE	195	147	145

Figure S4. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S5. 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	2	7	4	2
1P GAIN WILD-TYPE	97	51	40	63	101	62	73

Figure S5. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S6. Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
1P GAIN MUTATED	35	12	2
1P GAIN WILD-TYPE	188	138	155

Figure S6. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S7. Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
1P GAIN MUTATED	21	1	4	23
1P GAIN WILD-TYPE	198	57	133	93

Figure S7. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.005

Table S8. Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
1P GAIN MUTATED	30	6	8
1P GAIN WILD-TYPE	142	90	122

Figure S8. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00294 (Fisher's exact test), Q value = 0.0061

Table S9. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
1P GAIN MUTATED	26	6	12
1P GAIN WILD-TYPE	118	109	127

Figure S9. Get High-res Image Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.019

Table S10. 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	6	2	6	5	3
1Q GAIN WILD-TYPE	8	7	1	2	13

Figure S10. 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 = 3e-05

Table S11. Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1Q GAIN MUTATED	57	90	12	8	21
1Q GAIN WILD-TYPE	112	215	7	1	16

Figure S11. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #3: 'CN_CNMF'

'1q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.028

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
1Q GAIN MUTATED	16	25	23	5
1Q GAIN WILD-TYPE	51	42	20	12

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
1Q GAIN MUTATED	76	75	37
1Q GAIN WILD-TYPE	158	78	113

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00043

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	47	29	11	33	33	17	18
1Q GAIN WILD-TYPE	76	24	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 = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
1Q GAIN MUTATED	69	79	39
1Q GAIN WILD-TYPE	154	71	118

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.03

Table S16. Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
1Q GAIN MUTATED	77	30	38	42
1Q GAIN WILD-TYPE	142	28	99	74

Figure S16. Get High-res Image Gene #2: '1q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2P GAIN MUTATED	62	9	10	3	11
2P GAIN WILD-TYPE	107	296	9	6	26

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 = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
2P GAIN MUTATED	53	9	11
2P GAIN WILD-TYPE	112	80	160

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

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S19. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
2P GAIN MUTATED	70	15	10
2P GAIN WILD-TYPE	164	138	140

Figure S19. 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 = 3e-05

Table S20. 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	49	7	11	4	14	6	4
2P GAIN WILD-TYPE	74	46	36	61	94	60	71

Figure S20. 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 = 3e-05

Table S21. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
2P GAIN MUTATED	66	17	11
2P GAIN WILD-TYPE	157	133	146

Figure S21. 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 = 3e-05

Table S22. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
2P GAIN MUTATED	34	7	10	43
2P GAIN WILD-TYPE	185	51	127	73

Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00016

Table S23. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
2P GAIN MUTATED	42	20	8
2P GAIN WILD-TYPE	130	76	122

Figure S23. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.00043

Table S24. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
2P GAIN MUTATED	35	7	28
2P GAIN WILD-TYPE	109	108	111

Figure S24. 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 = 3e-05

Table S25. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2Q GAIN MUTATED	52	7	8	3	9
2Q GAIN WILD-TYPE	117	298	11	6	28

Figure S25. 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 = 3e-05

Table S26. Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
2Q GAIN MUTATED	47	7	10
2Q GAIN WILD-TYPE	118	82	161

Figure S26. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S27. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
2Q GAIN MUTATED	59	12	8
2Q GAIN WILD-TYPE	175	141	142

Figure S27. 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 = 3e-05

Table S28. 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	9	3	12	5	4
2Q GAIN WILD-TYPE	82	48	38	62	96	61	71

Figure S28. 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 = 3e-05

Table S29. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
2Q GAIN MUTATED	55	16	8
2Q GAIN WILD-TYPE	168	134	149

Figure S29. 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 = 3e-05

Table S30. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
2Q GAIN MUTATED	30	5	8	36
2Q GAIN WILD-TYPE	189	53	129	80

Figure S30. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00023

Table S31. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
2Q GAIN MUTATED	39	16	7
2Q GAIN WILD-TYPE	133	80	123

Figure S31. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-04 (Fisher's exact test), Q value = 0.00073

Table S32. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
2Q GAIN MUTATED	31	6	25
2Q GAIN WILD-TYPE	113	109	114

Figure S32. 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 = 3e-05

Table S33. Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3P GAIN MUTATED	31	2	1	3	12
3P GAIN WILD-TYPE	138	303	18	6	25

Figure S33. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #3: 'CN_CNMF'

'3p gain' versus 'METHLYATION_CNMF'

P value = 0.00926 (Fisher's exact test), Q value = 0.017

Table S34. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3P GAIN MUTATED	26	7	10
3P GAIN WILD-TYPE	139	82	161

Figure S34. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S35. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
3P GAIN MUTATED	35	4	10
3P GAIN WILD-TYPE	199	149	140

Figure S35. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00554 (Fisher's exact test), Q value = 0.011

Table S36. 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	14	3	4
3P GAIN WILD-TYPE	107	53	39	61	94	63	71

Figure S36. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S37. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
3P GAIN MUTATED	33	8	8
3P GAIN WILD-TYPE	190	142	149

Figure S37. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.0022

Table S38. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
3P GAIN MUTATED	18	0	11	20
3P GAIN WILD-TYPE	201	58	126	96

Figure S38. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0149 (Fisher's exact test), Q value = 0.027

Table S39. Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
3P GAIN MUTATED	25	9	6
3P GAIN WILD-TYPE	147	87	124

Figure S39. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.06

Table S40. Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
3P GAIN MUTATED	22	7	11
3P GAIN WILD-TYPE	122	108	128

Figure S40. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3Q GAIN MUTATED	62	4	2	3	13
3Q GAIN WILD-TYPE	107	301	17	6	24

Figure S41. 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 = 3e-05

Table S42. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3Q GAIN MUTATED	54	9	11
3Q GAIN WILD-TYPE	111	80	160

Figure S42. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S43. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
3Q GAIN MUTATED	68	5	11
3Q GAIN WILD-TYPE	166	148	139

Figure S43. 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 = 3e-05

Table S44. 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	37	0	18	4	17	3	5
3Q GAIN WILD-TYPE	86	53	29	61	91	63	70

Figure S44. 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 = 3e-05

Table S45. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
3Q GAIN MUTATED	63	12	9
3Q GAIN WILD-TYPE	160	138	148

Figure S45. 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 = 3e-05

Table S46. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
3Q GAIN MUTATED	30	0	12	42
3Q GAIN WILD-TYPE	189	58	125	74

Figure S46. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00068

Table S47. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
3Q GAIN MUTATED	43	17	10
3Q GAIN WILD-TYPE	129	79	120

Figure S47. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S48. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
3Q GAIN MUTATED	41	8	21
3Q GAIN WILD-TYPE	103	107	118

Figure S48. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S49. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4P GAIN MUTATED	13	0	0	0	1
4P GAIN WILD-TYPE	156	305	19	9	36

Figure S49. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0379 (Fisher's exact test), Q value = 0.063

Table S50. Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
4P GAIN MUTATED	5	0	0	0
4P GAIN WILD-TYPE	62	67	43	17

Figure S50. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S51. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
4P GAIN MUTATED	13	0	1
4P GAIN WILD-TYPE	221	153	149

Figure S51. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.072

Table S52. 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 S52. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.0081

Table S53. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
4P GAIN MUTATED	12	1	1
4P GAIN WILD-TYPE	211	149	156

Figure S53. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00055 (Fisher's exact test), Q value = 0.0013

Table S54. Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
4P GAIN MUTATED	3	0	1	10
4P GAIN WILD-TYPE	216	58	136	106

Figure S54. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 0.00457 (Fisher's exact test), Q value = 0.009

Table S55. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4Q GAIN MUTATED	7	0	0	0	1
4Q GAIN WILD-TYPE	162	305	19	9	36

Figure S55. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 0.0293 (Fisher's exact test), Q value = 0.05

Table S56. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
4Q GAIN MUTATED	7	0	1
4Q GAIN WILD-TYPE	227	153	149

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

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S57. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5P GAIN MUTATED	43	3	4	1	0
5P GAIN WILD-TYPE	126	302	15	8	37

Figure S57. 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 = 3e-05

Table S58. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5P GAIN MUTATED	34	5	5
5P GAIN WILD-TYPE	131	84	166

Figure S58. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S59. Gene #9: '5p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
5P GAIN MUTATED	45	5	1
5P GAIN WILD-TYPE	189	148	149

Figure S59. 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 = 3e-05

Table S60. 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	5	2	0
5P GAIN WILD-TYPE	95	50	35	64	103	64	75

Figure S60. 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 = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
5P GAIN MUTATED	40	10	1
5P GAIN WILD-TYPE	183	140	156

Figure S61. 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 = 3e-05

Table S62. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
5P GAIN MUTATED	13	4	1	33
5P GAIN WILD-TYPE	206	54	136	83

Figure S62. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00052

Table S63. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
5P GAIN MUTATED	30	8	4
5P GAIN WILD-TYPE	142	88	126

Figure S63. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S64. Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5P GAIN MUTATED	32	1	9
5P GAIN WILD-TYPE	112	114	130

Figure S64. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S65. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5Q GAIN MUTATED	15	1	3	1	0
5Q GAIN WILD-TYPE	154	304	16	8	37

Figure S65. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0357 (Fisher's exact test), Q value = 0.06

Table S66. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5Q GAIN MUTATED	13	2	4
5Q GAIN WILD-TYPE	152	87	167

Figure S66. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00061

Table S67. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
5Q GAIN MUTATED	17	3	0
5Q GAIN WILD-TYPE	217	150	150

Figure S67. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00652 (Fisher's exact test), Q value = 0.013

Table S68. 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 S68. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.0052

Table S69. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
5Q GAIN MUTATED	13	7	0
5Q GAIN WILD-TYPE	210	143	157

Figure S69. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00036

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
5Q GAIN MUTATED	6	2	0	12
5Q GAIN WILD-TYPE	213	56	137	104

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

'5q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00031

Table S71. Gene #10: '5q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5Q GAIN MUTATED	14	0	3
5Q GAIN WILD-TYPE	130	115	136

Figure S71. 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 = 3e-05

Table S72. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6P GAIN MUTATED	61	5	1	1	12
6P GAIN WILD-TYPE	108	300	18	8	25

Figure S72. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

'6p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S73. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
6P GAIN MUTATED	49	12	11
6P GAIN WILD-TYPE	116	77	160

Figure S73. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S74. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
6P GAIN MUTATED	61	5	14
6P GAIN WILD-TYPE	173	148	136

Figure S74. 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 = 3e-05

Table S75. 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	43	0	5	5	14	8	5
6P GAIN WILD-TYPE	80	53	42	60	94	58	70

Figure S75. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S76. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
6P GAIN MUTATED	55	14	11
6P GAIN WILD-TYPE	168	136	146

Figure S76. 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 = 3e-05

Table S77. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
6P GAIN MUTATED	34	0	11	35
6P GAIN WILD-TYPE	185	58	126	81

Figure S77. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.0044

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
6P GAIN MUTATED	42	15	12
6P GAIN WILD-TYPE	130	81	118

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

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0194 (Fisher's exact test), Q value = 0.034

Table S79. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
6P GAIN MUTATED	34	12	23
6P GAIN WILD-TYPE	110	103	116

Figure S79. 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 = 3e-05

Table S80. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6Q GAIN MUTATED	46	5	1	1	11
6Q GAIN WILD-TYPE	123	300	18	8	26

Figure S80. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S81. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
6Q GAIN MUTATED	35	9	12
6Q GAIN WILD-TYPE	130	80	159

Figure S81. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S82. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
6Q GAIN MUTATED	45	5	14
6Q GAIN WILD-TYPE	189	148	136

Figure S82. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S83. 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	6	5	12	7	6
6Q GAIN WILD-TYPE	95	53	41	60	96	59	69

Figure S83. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.0022

Table S84. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
6Q GAIN MUTATED	41	12	11
6Q GAIN WILD-TYPE	182	138	146

Figure S84. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S85. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
6Q GAIN MUTATED	29	0	11	24
6Q GAIN WILD-TYPE	190	58	126	92

Figure S85. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.028

Table S86. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
6Q GAIN MUTATED	31	13	9
6Q GAIN WILD-TYPE	141	83	121

Figure S86. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S87. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7P GAIN MUTATED	33	9	12	2	11
7P GAIN WILD-TYPE	136	296	7	7	26

Figure S87. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.0029

Table S88. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
7P GAIN MUTATED	30	3	18
7P GAIN WILD-TYPE	135	86	153

Figure S88. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.064

Table S89. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
7P GAIN MUTATED	39	15	13
7P GAIN WILD-TYPE	195	138	137

Figure S89. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.024

Table S90. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
7P GAIN MUTATED	36	20	10
7P GAIN WILD-TYPE	187	130	147

Figure S90. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.052

Table S91. Gene #13: '7p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
7P GAIN MUTATED	26	14	8
7P GAIN WILD-TYPE	146	82	122

Figure S91. 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 = 3e-05

Table S92. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7Q GAIN MUTATED	30	12	12	2	10
7Q GAIN WILD-TYPE	139	293	7	7	27

Figure S92. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.0032

Table S93. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
7Q GAIN MUTATED	27	2	21
7Q GAIN WILD-TYPE	138	87	150

Figure S93. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.047

Table S94. 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	20	8	8	1	15	8	6
7Q GAIN WILD-TYPE	103	45	39	64	93	58	69

Figure S94. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S95. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8P GAIN MUTATED	43	29	8	2	36
8P GAIN WILD-TYPE	126	276	11	7	1

Figure S95. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'RPPA_CNMF'

P value = 0.0214 (Fisher's exact test), Q value = 0.037

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
8P GAIN MUTATED	7	10	4	2	2	8
8P GAIN WILD-TYPE	34	27	35	10	39	16

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

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.06

Table S97. Gene #15: '8p 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
8P GAIN MUTATED	28	10	11	8	34	17	10
8P GAIN WILD-TYPE	95	43	36	57	74	49	65

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

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 0.05

Table S98. Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
8P GAIN MUTATED	60	6	27	24
8P GAIN WILD-TYPE	159	52	110	92

Figure S98. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MRNA_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.019

Table S99. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
8Q GAIN MUTATED	1	8	2	0
8Q GAIN WILD-TYPE	13	9	10	10

Figure S99. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.052

Table S100. 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 S100. 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 = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8Q GAIN MUTATED	80	31	8	3	37
8Q GAIN WILD-TYPE	89	274	11	6	0

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

'8q gain' versus 'METHLYATION_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.065

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
8Q GAIN MUTATED	64	24	46
8Q GAIN WILD-TYPE	101	65	125

Figure S102. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.00073

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
8Q GAIN MUTATED	9	12	7	2	2	13
8Q GAIN WILD-TYPE	32	25	32	10	39	11

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

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.038

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
8Q GAIN MUTATED	15	15	6	9
8Q GAIN WILD-TYPE	52	52	37	8

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

'8q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
8Q GAIN MUTATED	97	28	34
8Q GAIN WILD-TYPE	137	125	116

Figure S105. 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 = 3e-05

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

'8q gain' versus 'MIRSEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00048

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
8Q GAIN MUTATED	87	36	33
8Q GAIN WILD-TYPE	136	114	124

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

'8q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
8Q GAIN MUTATED	68	6	31	51
8Q GAIN WILD-TYPE	151	52	106	65

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

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S109. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
8Q GAIN MUTATED	71	28	27
8Q GAIN WILD-TYPE	101	68	103

Figure S109. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.014

Table S110. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
8Q GAIN MUTATED	59	27	40
8Q GAIN WILD-TYPE	85	88	99

Figure S110. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00018

Table S111. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9P GAIN MUTATED	18	3	0	0	1
9P GAIN WILD-TYPE	151	302	19	9	36

Figure S111. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.0076

Table S112. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
9P GAIN MUTATED	15	2	3
9P GAIN WILD-TYPE	150	87	168

Figure S112. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 0.00501 (Fisher's exact test), Q value = 0.0098

Table S113. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
9P GAIN MUTATED	17	2	3
9P GAIN WILD-TYPE	217	151	147

Figure S113. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0132 (Fisher's exact test), Q value = 0.024

Table S114. 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	11	0	1	1	7	2	0
9P GAIN WILD-TYPE	112	53	46	64	101	64	75

Figure S114. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.02

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
9P GAIN MUTATED	16	4	2
9P GAIN WILD-TYPE	207	146	155

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

'9q gain' versus 'CN_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.052

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9Q GAIN MUTATED	7	1	0	0	1
9Q GAIN WILD-TYPE	162	304	19	9	36

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

'10p gain' versus 'MRNA_CNMF'

P value = 0.0077 (Fisher's exact test), Q value = 0.015

Table S117. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
10P GAIN MUTATED	2	2	8	2
10P GAIN WILD-TYPE	12	15	4	8

Figure S117. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S118. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10P GAIN MUTATED	41	46	7	4	19
10P GAIN WILD-TYPE	128	259	12	5	18

Figure S118. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.033

Table S119. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
10P GAIN MUTATED	35	17	39	26
10P GAIN WILD-TYPE	184	41	98	90

Figure S119. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.06

Table S120. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
10P GAIN MUTATED	24	33	24
10P GAIN WILD-TYPE	120	82	115

Figure S120. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00495 (Fisher's exact test), Q value = 0.0097

Table S121. Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
10Q GAIN MUTATED	1	3	8	2
10Q GAIN WILD-TYPE	13	14	4	8

Figure S121. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S122. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10Q GAIN MUTATED	36	45	8	4	16
10Q GAIN WILD-TYPE	133	260	11	5	21

Figure S122. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00195 (Fisher's exact test), Q value = 0.0042

Table S123. Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
10Q GAIN MUTATED	29	17	38	25
10Q GAIN WILD-TYPE	190	41	99	91

Figure S123. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MRNA_CNMF'

P value = 0.0392 (Fisher's exact test), Q value = 0.064

Table S124. Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
11P GAIN MUTATED	0	4	0	0
11P GAIN WILD-TYPE	14	13	12	10

Figure S124. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S125. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11P GAIN MUTATED	17	0	4	0	2
11P GAIN WILD-TYPE	152	305	15	9	35

Figure S125. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.071

Table S126. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
11P GAIN MUTATED	12	4	3
11P GAIN WILD-TYPE	153	85	168

Figure S126. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00327 (Fisher's exact test), Q value = 0.0067

Table S127. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
11P GAIN MUTATED	18	2	3
11P GAIN WILD-TYPE	216	151	147

Figure S127. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00149 (Fisher's exact test), Q value = 0.0032

Table S128. 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 S128. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00223 (Fisher's exact test), Q value = 0.0047

Table S129. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
11P GAIN MUTATED	18	2	3
11P GAIN WILD-TYPE	205	148	154

Figure S129. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.013

Table S130. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
11P GAIN MUTATED	8	1	2	12
11P GAIN WILD-TYPE	211	57	135	104

Figure S130. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S131. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11Q GAIN MUTATED	13	0	3	0	3
11Q GAIN WILD-TYPE	156	305	16	9	34

Figure S131. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.021

Table S132. Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
11Q GAIN MUTATED	1	4	0	3
11Q GAIN WILD-TYPE	66	63	43	14

Figure S132. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.056

Table S133. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
11Q GAIN MUTATED	14	2	3
11Q GAIN WILD-TYPE	220	151	147

Figure S133. 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 = 3e-05

Table S134. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12P GAIN MUTATED	42	14	7	3	5
12P GAIN WILD-TYPE	127	291	12	6	32

Figure S134. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S135. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12P GAIN MUTATED	35	14	8
12P GAIN WILD-TYPE	130	75	163

Figure S135. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S136. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
12P GAIN MUTATED	51	10	10
12P GAIN WILD-TYPE	183	143	140

Figure S136. 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 = 0.00011

Table S137. 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	13	3	7
12P GAIN WILD-TYPE	92	52	37	59	95	63	68

Figure S137. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.0013

Table S138. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
12P GAIN MUTATED	44	17	10
12P GAIN WILD-TYPE	179	133	147

Figure S138. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S139. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
12P GAIN MUTATED	29	4	10	28
12P GAIN WILD-TYPE	190	54	127	88

Figure S139. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00402 (Fisher's exact test), Q value = 0.008

Table S140. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
12P GAIN MUTATED	34	11	9
12P GAIN WILD-TYPE	138	85	121

Figure S140. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00346 (Fisher's exact test), Q value = 0.0071

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
12P GAIN MUTATED	29	7	18
12P GAIN WILD-TYPE	115	108	121

Figure S141. 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 = 3e-05

Table S142. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12Q GAIN MUTATED	26	14	6	3	5
12Q GAIN WILD-TYPE	143	291	13	6	32

Figure S142. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

P value = 0.0088 (Fisher's exact test), Q value = 0.016

Table S143. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12Q GAIN MUTATED	22	12	8
12Q GAIN WILD-TYPE	143	77	163

Figure S143. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 0.00439 (Fisher's exact test), Q value = 0.0087

Table S144. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
12Q GAIN MUTATED	35	9	10
12Q GAIN WILD-TYPE	199	144	140

Figure S144. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0422 (Fisher's exact test), Q value = 0.068

Table S145. Gene #24: '12q 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
12Q GAIN MUTATED	19	1	8	6	10	3	7
12Q GAIN WILD-TYPE	104	52	39	59	98	63	68

Figure S145. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.0486 (Fisher's exact test), Q value = 0.077

Table S146. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
12Q GAIN MUTATED	31	13	10
12Q GAIN WILD-TYPE	192	137	147

Figure S146. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.013

Table S147. 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 S147. 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 = 3e-05

Table S148. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
13Q GAIN MUTATED	27	0	0	1	2
13Q GAIN WILD-TYPE	142	305	19	8	35

Figure S148. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00016

Table S149. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
13Q GAIN MUTATED	18	7	1
13Q GAIN WILD-TYPE	147	82	170

Figure S149. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.021

Table S150. Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
13Q GAIN MUTATED	4	1	0	3
13Q GAIN WILD-TYPE	63	66	43	14

Figure S150. 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 = 3e-05

Table S151. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
13Q GAIN MUTATED	27	1	2
13Q GAIN WILD-TYPE	207	152	148

Figure S151. 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 = 3e-05

Table S152. 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 S152. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S153. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
13Q GAIN MUTATED	27	1	2
13Q GAIN WILD-TYPE	196	149	155

Figure S153. 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 = 3e-05

Table S154. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
13Q GAIN MUTATED	5	0	2	23
13Q GAIN WILD-TYPE	214	58	135	93

Figure S154. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.013

Table S155. Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
13Q GAIN MUTATED	17	6	2
13Q GAIN WILD-TYPE	155	90	128

Figure S155. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0236 (Fisher's exact test), Q value = 0.041

Table S156. Gene #25: '13q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
13Q GAIN MUTATED	14	2	9
13Q GAIN WILD-TYPE	130	113	130

Figure S156. 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 = 3e-05

Table S157. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
14Q GAIN MUTATED	26	4	1	0	6
14Q GAIN WILD-TYPE	143	301	18	9	31

Figure S157. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00215 (Fisher's exact test), Q value = 0.0045

Table S158. Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
14Q GAIN MUTATED	23	4	7
14Q GAIN WILD-TYPE	142	85	164

Figure S158. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00057

Table S159. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
14Q GAIN MUTATED	28	3	6
14Q GAIN WILD-TYPE	206	150	144

Figure S159. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S160. 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	17	1	6	1	8	0	4
14Q GAIN WILD-TYPE	106	52	41	64	100	66	71

Figure S160. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

P value = 0.0062 (Fisher's exact test), Q value = 0.012

Table S161. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
14Q GAIN MUTATED	25	6	6
14Q GAIN WILD-TYPE	198	144	151

Figure S161. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.0011

Table S162. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
14Q GAIN MUTATED	10	1	7	19
14Q GAIN WILD-TYPE	209	57	130	97

Figure S162. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'CN_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.0013

Table S163. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
15Q GAIN MUTATED	8	0	1	0	2
15Q GAIN WILD-TYPE	161	305	18	9	35

Figure S163. 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 = 3e-05

Table S164. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16P GAIN MUTATED	22	1	1	0	3
16P GAIN WILD-TYPE	147	304	18	9	34

Figure S164. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.0051

Table S165. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
16P GAIN MUTATED	16	0	9
16P GAIN WILD-TYPE	149	89	162

Figure S165. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.033

Table S166. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
16P GAIN MUTATED	19	4	4
16P GAIN WILD-TYPE	215	149	146

Figure S166. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.0069

Table S167. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
16P GAIN MUTATED	20	3	4
16P GAIN WILD-TYPE	203	147	153

Figure S167. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q gain' versus 'CN_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.022

Table S168. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16Q GAIN MUTATED	8	1	0	0	1
16Q GAIN WILD-TYPE	161	304	19	9	36

Figure S168. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'CN_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0032

Table S169. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17P GAIN MUTATED	8	1	0	1	2
17P GAIN WILD-TYPE	161	304	19	8	35

Figure S169. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0413 (Fisher's exact test), Q value = 0.067

Table S170. 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	8	0	1	1	2	0	0
17P GAIN WILD-TYPE	115	53	46	64	106	66	75

Figure S170. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S171. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17Q GAIN MUTATED	25	1	0	1	3
17Q GAIN WILD-TYPE	144	304	19	8	34

Figure S171. 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 = 3e-05

Table S172. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
17Q GAIN MUTATED	23	2	2
17Q GAIN WILD-TYPE	142	87	169

Figure S172. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.067

Table S173. Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
17Q GAIN MUTATED	4	1	0	1	0	0
17Q GAIN WILD-TYPE	37	36	39	11	41	24

Figure S173. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S174. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
17Q GAIN MUTATED	25	2	3
17Q GAIN WILD-TYPE	209	151	147

Figure S174. 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 = 3e-05

Table S175. 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 S175. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00031

Table S176. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
17Q GAIN MUTATED	24	3	3
17Q GAIN WILD-TYPE	199	147	154

Figure S176. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0022 (Fisher's exact test), Q value = 0.0046

Table S177. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
17Q GAIN MUTATED	11	1	3	15
17Q GAIN WILD-TYPE	208	57	134	101

Figure S177. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S178. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18P GAIN MUTATED	65	3	3	0	1
18P GAIN WILD-TYPE	104	302	16	9	36

Figure S178. 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 = 3e-05

Table S179. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18P GAIN MUTATED	45	13	4
18P GAIN WILD-TYPE	120	76	167

Figure S179. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.022

Table S180. Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
18P GAIN MUTATED	7	3	0	0	1	4
18P GAIN WILD-TYPE	34	34	39	12	40	20

Figure S180. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S181. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
18P GAIN MUTATED	65	3	4
18P GAIN WILD-TYPE	169	150	146

Figure S181. 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 = 3e-05

Table S182. 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	47	1	13	1	7	2	1
18P GAIN WILD-TYPE	76	52	34	64	101	64	74

Figure S182. 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 = 3e-05

Table S183. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
18P GAIN MUTATED	60	9	3
18P GAIN WILD-TYPE	163	141	154

Figure S183. 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 = 3e-05

Table S184. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
18P GAIN MUTATED	24	1	2	45
18P GAIN WILD-TYPE	195	57	135	71

Figure S184. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S185. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
18P GAIN MUTATED	40	16	3
18P GAIN WILD-TYPE	132	80	127

Figure S185. 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 = 3e-05

Table S186. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
18P GAIN MUTATED	33	2	24
18P GAIN WILD-TYPE	111	113	115

Figure S186. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0432 (Fisher's exact test), Q value = 0.069

Table S187. Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
18Q GAIN MUTATED	0	3	0	0	1
18Q GAIN WILD-TYPE	14	6	7	7	15

Figure S187. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S188. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18Q GAIN MUTATED	39	3	2	0	1
18Q GAIN WILD-TYPE	130	302	17	9	36

Figure S188. 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 = 3e-05

Table S189. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18Q GAIN MUTATED	29	7	3
18Q GAIN WILD-TYPE	136	82	168

Figure S189. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S190. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
18Q GAIN MUTATED	40	2	3
18Q GAIN WILD-TYPE	194	151	147

Figure S190. 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 = 3e-05

Table S191. 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	30	1	5	0	6	2	1
18Q GAIN WILD-TYPE	93	52	42	65	102	64	74

Figure S191. 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 = 3e-05

Table S192. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
18Q GAIN MUTATED	35	9	1
18Q GAIN WILD-TYPE	188	141	156

Figure S192. 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 = 3e-05

Table S193. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
18Q GAIN MUTATED	19	1	1	24
18Q GAIN WILD-TYPE	200	57	136	92

Figure S193. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S194. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
18Q GAIN MUTATED	27	8	1
18Q GAIN WILD-TYPE	145	88	129

Figure S194. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00026

Table S195. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
18Q GAIN MUTATED	22	1	13
18Q GAIN WILD-TYPE	122	114	126

Figure S195. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.0393 (Fisher's exact test), Q value = 0.064

Table S196. Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
19P GAIN MUTATED	0	4	0	0
19P GAIN WILD-TYPE	14	13	12	10

Figure S196. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.051

Table S197. 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 S197. 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 = 3e-05

Table S198. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19P GAIN MUTATED	49	0	1	0	4
19P GAIN WILD-TYPE	120	305	18	9	33

Figure S198. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.00066

Table S199. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19P GAIN MUTATED	30	11	8
19P GAIN WILD-TYPE	135	78	163

Figure S199. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S200. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
19P GAIN MUTATED	47	2	4
19P GAIN WILD-TYPE	187	151	146

Figure S200. 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 = 3e-05

Table S201. 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	36	1	3	2	8	2	1
19P GAIN WILD-TYPE	87	52	44	63	100	64	74

Figure S201. 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 = 3e-05

Table S202. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
19P GAIN MUTATED	45	4	5
19P GAIN WILD-TYPE	178	146	152

Figure S202. 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 = 3e-05

Table S203. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
19P GAIN MUTATED	17	1	6	30
19P GAIN WILD-TYPE	202	57	131	86

Figure S203. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00095

Table S204. Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
19P GAIN MUTATED	28	14	4
19P GAIN WILD-TYPE	144	82	126

Figure S204. 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 = 3e-05

Table S205. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19Q GAIN MUTATED	51	0	2	0	4
19Q GAIN WILD-TYPE	118	305	17	9	33

Figure S205. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S206. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19Q GAIN MUTATED	33	11	7
19Q GAIN WILD-TYPE	132	78	164

Figure S206. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0431 (Fisher's exact test), Q value = 0.069

Table S207. Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
19Q GAIN MUTATED	5	1	0	2
19Q GAIN WILD-TYPE	62	66	43	15

Figure S207. 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 = 3e-05

Table S208. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
19Q GAIN MUTATED	52	2	3
19Q GAIN WILD-TYPE	182	151	147

Figure S208. 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 = 3e-05

Table S209. 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	39	1	6	1	8	1	1
19Q GAIN WILD-TYPE	84	52	41	64	100	65	74

Figure S209. 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 = 3e-05

Table S210. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
19Q GAIN MUTATED	48	5	4
19Q GAIN WILD-TYPE	175	145	153

Figure S210. 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 = 3e-05

Table S211. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
19Q GAIN MUTATED	14	1	5	37
19Q GAIN WILD-TYPE	205	57	132	79

Figure S211. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00052

Table S212. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
19Q GAIN MUTATED	29	15	4
19Q GAIN WILD-TYPE	143	81	126

Figure S212. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0136 (Fisher's exact test), Q value = 0.024

Table S213. Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
19Q GAIN MUTATED	24	6	18
19Q GAIN WILD-TYPE	120	109	121

Figure S213. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00803 (Fisher's exact test), Q value = 0.015

Table S214. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
20P GAIN MUTATED	0	5	0	0
20P GAIN WILD-TYPE	14	12	12	10

Figure S214. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0494 (Fisher's exact test), Q value = 0.078

Table S215. Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
20P GAIN MUTATED	2	3	0	0	0
20P GAIN WILD-TYPE	12	6	7	7	16

Figure S215. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S216. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20P GAIN MUTATED	85	7	12	2	6
20P GAIN WILD-TYPE	84	298	7	7	31

Figure S216. 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 = 3e-05

Table S217. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
20P GAIN MUTATED	73	13	17
20P GAIN WILD-TYPE	92	76	154

Figure S217. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S218. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
20P GAIN MUTATED	89	9	14
20P GAIN WILD-TYPE	145	144	136

Figure S218. 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 = 3e-05

Table S219. 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	62	4	15	2	15	12	2
20P GAIN WILD-TYPE	61	49	32	63	93	54	73

Figure S219. 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 = 3e-05

Table S220. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
20P GAIN MUTATED	81	16	14
20P GAIN WILD-TYPE	142	134	143

Figure S220. 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 = 3e-05

Table S221. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
20P GAIN MUTATED	36	5	13	57
20P GAIN WILD-TYPE	183	53	124	59

Figure S221. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00061

Table S222. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
20P GAIN MUTATED	58	20	18
20P GAIN WILD-TYPE	114	76	112

Figure S222. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S223. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
20P GAIN MUTATED	56	15	25
20P GAIN WILD-TYPE	88	100	114

Figure S223. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 0.00198 (Fisher's exact test), Q value = 0.0042

Table S224. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
20Q GAIN MUTATED	0	6	0	0
20Q GAIN WILD-TYPE	14	11	12	10

Figure S224. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00711 (Fisher's exact test), Q value = 0.014

Table S225. Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
20Q GAIN MUTATED	2	4	0	0	0
20Q GAIN WILD-TYPE	12	5	7	7	16

Figure S225. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S226. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20Q GAIN MUTATED	103	8	12	2	7
20Q GAIN WILD-TYPE	66	297	7	7	30

Figure S226. 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 = 3e-05

Table S227. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
20Q GAIN MUTATED	83	16	21
20Q GAIN WILD-TYPE	82	73	150

Figure S227. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'RPPA_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.054

Table S228. Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
20Q GAIN MUTATED	6	8	2	0	2	6
20Q GAIN WILD-TYPE	35	29	37	12	39	18

Figure S228. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S229. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
20Q GAIN MUTATED	104	10	18
20Q GAIN WILD-TYPE	130	143	132

Figure S229. 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 = 3e-05

Table S230. 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	71	4	19	3	18	14	3
20Q GAIN WILD-TYPE	52	49	28	62	90	52	72

Figure S230. 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 = 3e-05

Table S231. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
20Q GAIN MUTATED	95	17	18
20Q GAIN WILD-TYPE	128	133	139

Figure S231. 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 = 3e-05

Table S232. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
20Q GAIN MUTATED	43	5	17	65
20Q GAIN WILD-TYPE	176	53	120	51

Figure S232. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S233. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
20Q GAIN MUTATED	70	23	19
20Q GAIN WILD-TYPE	102	73	111

Figure S233. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S234. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
20Q GAIN MUTATED	64	18	30
20Q GAIN WILD-TYPE	80	97	109

Figure S234. 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 = 3e-05

Table S235. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
21Q GAIN MUTATED	35	1	0	0	3
21Q GAIN WILD-TYPE	134	304	19	9	34

Figure S235. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S236. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
21Q GAIN MUTATED	24	7	5
21Q GAIN WILD-TYPE	141	82	166

Figure S236. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S237. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
21Q GAIN MUTATED	33	2	4
21Q GAIN WILD-TYPE	201	151	146

Figure S237. 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 = 3e-05

Table S238. 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 S238. 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 = 3e-05

Table S239. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
21Q GAIN MUTATED	34	2	3
21Q GAIN WILD-TYPE	189	148	154

Figure S239. 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 = 3e-05

Table S240. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
21Q GAIN MUTATED	9	1	4	25
21Q GAIN WILD-TYPE	210	57	133	91

Figure S240. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.00082

Table S241. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
21Q GAIN MUTATED	23	10	2
21Q GAIN WILD-TYPE	149	86	128

Figure S241. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S242. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
22Q GAIN MUTATED	27	3	0	1	0
22Q GAIN WILD-TYPE	142	302	19	8	37

Figure S242. 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 = 3e-05

Table S243. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
22Q GAIN MUTATED	26	1	1
22Q GAIN WILD-TYPE	139	88	170

Figure S243. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S244. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
22Q GAIN MUTATED	31	0	0
22Q GAIN WILD-TYPE	203	153	150

Figure S244. 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 = 3e-05

Table S245. 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	16	0	12	0	3	0	0
22Q GAIN WILD-TYPE	107	53	35	65	105	66	75

Figure S245. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S246. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
22Q GAIN MUTATED	28	1	1
22Q GAIN WILD-TYPE	195	149	156

Figure S246. 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 = 3e-05

Table S247. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
22Q GAIN MUTATED	9	0	1	20
22Q GAIN WILD-TYPE	210	58	136	96

Figure S247. 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 = 0.00011

Table S248. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
22Q GAIN MUTATED	24	2	2
22Q GAIN WILD-TYPE	148	94	128

Figure S248. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S249. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
22Q GAIN MUTATED	22	1	5
22Q GAIN WILD-TYPE	122	114	134

Figure S249. 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 = 3e-05

Table S250. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
XP GAIN MUTATED	23	7	8	3	23
XP GAIN WILD-TYPE	146	298	11	6	14

Figure S250. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S251. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
XQ GAIN MUTATED	24	7	8	3	22
XQ GAIN WILD-TYPE	145	298	11	6	15

Figure S251. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S252. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1P LOSS MUTATED	18	0	3	4	0
1P LOSS WILD-TYPE	151	305	16	5	37

Figure S252. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S253. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
1P LOSS MUTATED	20	1	0
1P LOSS WILD-TYPE	145	88	171

Figure S253. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S254. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
1P LOSS MUTATED	23	1	1
1P LOSS WILD-TYPE	211	152	149

Figure S254. 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 = 3e-05

Table S255. 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	13	1	7	0	4	0	0
1P LOSS WILD-TYPE	110	52	40	65	104	66	75

Figure S255. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00021

Table S256. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
1P LOSS MUTATED	21	3	1
1P LOSS WILD-TYPE	202	147	156

Figure S256. 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 = 3e-05

Table S257. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
1P LOSS MUTATED	6	0	0	19
1P LOSS WILD-TYPE	213	58	137	97

Figure S257. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.0014

Table S258. Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
1P LOSS MUTATED	14	0	8
1P LOSS WILD-TYPE	130	115	131

Figure S258. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S259. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
1Q LOSS MUTATED	12	0	1	1	0
1Q LOSS WILD-TYPE	157	305	18	8	37

Figure S259. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S260. Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
1Q LOSS MUTATED	12	0	0
1Q LOSS WILD-TYPE	153	89	171

Figure S260. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00021

Table S261. Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
1Q LOSS MUTATED	14	0	0
1Q LOSS WILD-TYPE	220	153	150

Figure S261. 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 = 0.0024

Table S262. 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	7	0	5	0	2	0	0
1Q LOSS WILD-TYPE	116	53	42	65	106	66	75

Figure S262. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.00077

Table S263. Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
1Q LOSS MUTATED	13	1	0
1Q LOSS WILD-TYPE	210	149	157

Figure S263. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S264. Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
1Q LOSS MUTATED	2	0	0	12
1Q LOSS WILD-TYPE	217	58	137	104

Figure S264. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0075 (Fisher's exact test), Q value = 0.014

Table S265. Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
1Q LOSS MUTATED	9	0	3
1Q LOSS WILD-TYPE	135	115	136

Figure S265. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.00059

Table S266. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2P LOSS MUTATED	10	0	1	0	0
2P LOSS WILD-TYPE	159	305	18	9	37

Figure S266. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 0.00533 (Fisher's exact test), Q value = 0.01

Table S267. Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
2P LOSS MUTATED	10	0	1
2P LOSS WILD-TYPE	224	153	149

Figure S267. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S268. Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
2Q LOSS MUTATED	16	0	1	0	0
2Q LOSS WILD-TYPE	153	305	18	9	37

Figure S268. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.00068

Table S269. Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
2Q LOSS MUTATED	15	0	2
2Q LOSS WILD-TYPE	219	153	148

Figure S269. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.026

Table S270. 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	9	0	1	0	6	1	0
2Q LOSS WILD-TYPE	114	53	46	65	102	65	75

Figure S270. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.032

Table S271. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
2Q LOSS MUTATED	13	2	2
2Q LOSS WILD-TYPE	210	148	155

Figure S271. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.051

Table S272. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
2Q LOSS MUTATED	5	0	3	9
2Q LOSS WILD-TYPE	214	58	134	107

Figure S272. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MRNA_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.063

Table S273. Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
3P LOSS MUTATED	0	4	0	0
3P LOSS WILD-TYPE	14	13	12	10

Figure S273. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0016

Table S274. 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 S274. 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 = 3e-05

Table S275. Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3P LOSS MUTATED	45	0	3	2	1
3P LOSS WILD-TYPE	124	305	16	7	36

Figure S275. 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 = 3e-05

Table S276. Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3P LOSS MUTATED	33	6	3
3P LOSS WILD-TYPE	132	83	168

Figure S276. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.039

Table S277. Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
3P LOSS MUTATED	2	8	1	0	1	2
3P LOSS WILD-TYPE	39	29	38	12	40	22

Figure S277. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S278. Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
3P LOSS MUTATED	47	1	2
3P LOSS WILD-TYPE	187	152	148

Figure S278. 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 = 3e-05

Table S279. 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	6	2	0
3P LOSS WILD-TYPE	87	53	41	65	102	64	75

Figure S279. 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 = 3e-05

Table S280. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
3P LOSS MUTATED	38	8	3
3P LOSS WILD-TYPE	185	142	154

Figure S280. 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 = 3e-05

Table S281. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
3P LOSS MUTATED	19	1	2	27
3P LOSS WILD-TYPE	200	57	135	89

Figure S281. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0151 (Fisher's exact test), Q value = 0.027

Table S282. Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
3P LOSS MUTATED	25	9	6
3P LOSS WILD-TYPE	147	87	124

Figure S282. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-04 (Fisher's exact test), Q value = 0.00026

Table S283. Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
3P LOSS MUTATED	26	3	11
3P LOSS WILD-TYPE	118	112	128

Figure S283. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.063

Table S284. Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
3Q LOSS MUTATED	0	4	0	0
3Q LOSS WILD-TYPE	14	13	12	10

Figure S284. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.0016

Table S285. 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 S285. 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 = 3e-05

Table S286. Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
3Q LOSS MUTATED	27	0	1	2	1
3Q LOSS WILD-TYPE	142	305	18	7	36

Figure S286. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S287. Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
3Q LOSS MUTATED	20	3	2
3Q LOSS WILD-TYPE	145	86	169

Figure S287. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S288. Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
3Q LOSS MUTATED	28	0	2
3Q LOSS WILD-TYPE	206	153	148

Figure S288. 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 = 3e-05

Table S289. 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	21	0	4	0	3	2	0
3Q LOSS WILD-TYPE	102	53	43	65	105	64	75

Figure S289. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S290. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
3Q LOSS MUTATED	25	1	3
3Q LOSS WILD-TYPE	198	149	154

Figure S290. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00045

Table S291. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
3Q LOSS MUTATED	12	0	2	15
3Q LOSS WILD-TYPE	207	58	135	101

Figure S291. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.023

Table S292. Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
3Q LOSS MUTATED	16	7	2
3Q LOSS WILD-TYPE	156	89	128

Figure S292. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MRNA_CNMF'

P value = 0.0037 (Fisher's exact test), Q value = 0.0075

Table S293. Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
4P LOSS MUTATED	1	7	0	0
4P LOSS WILD-TYPE	13	10	12	10

Figure S293. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00163 (Fisher's exact test), Q value = 0.0035

Table S294. 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 S294. 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 = 3e-05

Table S295. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4P LOSS MUTATED	91	4	4	4	2
4P LOSS WILD-TYPE	78	301	15	5	35

Figure S295. 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 = 3e-05

Table S296. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
4P LOSS MUTATED	72	16	6
4P LOSS WILD-TYPE	93	73	165

Figure S296. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 0.00106 (Fisher's exact test), Q value = 0.0023

Table S297. Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
4P LOSS MUTATED	5	8	0	1	1	6
4P LOSS WILD-TYPE	36	29	39	11	40	18

Figure S297. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S298. Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
4P LOSS MUTATED	91	6	8
4P LOSS WILD-TYPE	143	147	142

Figure S298. 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 = 3e-05

Table S299. 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	62	2	15	2	18	5	1
4P LOSS WILD-TYPE	61	51	32	63	90	61	74

Figure S299. 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 = 3e-05

Table S300. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
4P LOSS MUTATED	81	14	8
4P LOSS WILD-TYPE	142	136	149

Figure S300. 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 = 3e-05

Table S301. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
4P LOSS MUTATED	38	1	5	59
4P LOSS WILD-TYPE	181	57	132	57

Figure S301. 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 = 3e-05

Table S302. Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
4P LOSS MUTATED	55	26	12
4P LOSS WILD-TYPE	117	70	118

Figure S302. 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 = 3e-05

Table S303. Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
4P LOSS MUTATED	52	9	32
4P LOSS WILD-TYPE	92	106	107

Figure S303. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00513 (Fisher's exact test), Q value = 0.01

Table S304. 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	1	4	0	0	0
4Q LOSS WILD-TYPE	13	5	7	7	16

Figure S304. 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 = 3e-05

Table S305. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
4Q LOSS MUTATED	92	3	4	4	2
4Q LOSS WILD-TYPE	77	302	15	5	35

Figure S305. 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 = 3e-05

Table S306. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
4Q LOSS MUTATED	73	15	5
4Q LOSS WILD-TYPE	92	74	166

Figure S306. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.024

Table S307. Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
4Q LOSS MUTATED	5	7	1	1	1	6
4Q LOSS WILD-TYPE	36	30	38	11	40	18

Figure S307. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S308. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
4Q LOSS MUTATED	91	6	8
4Q LOSS WILD-TYPE	143	147	142

Figure S308. 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 = 3e-05

Table S309. 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	13	2	17	6	0
4Q LOSS WILD-TYPE	58	51	34	63	91	60	75

Figure S309. 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 = 3e-05

Table S310. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
4Q LOSS MUTATED	82	13	8
4Q LOSS WILD-TYPE	141	137	149

Figure S310. 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 = 3e-05

Table S311. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
4Q LOSS MUTATED	39	1	4	59
4Q LOSS WILD-TYPE	180	57	133	57

Figure S311. 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 = 3e-05

Table S312. Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
4Q LOSS MUTATED	53	28	11
4Q LOSS WILD-TYPE	119	68	119

Figure S312. 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 = 3e-05

Table S313. Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
4Q LOSS MUTATED	49	8	35
4Q LOSS WILD-TYPE	95	107	104

Figure S313. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.064

Table S314. 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 S314. 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 = 3e-05

Table S315. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5P LOSS MUTATED	46	0	3	2	4
5P LOSS WILD-TYPE	123	305	16	7	33

Figure S315. 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 = 3e-05

Table S316. Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5P LOSS MUTATED	38	5	2
5P LOSS WILD-TYPE	127	84	169

Figure S316. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 0.00378 (Fisher's exact test), Q value = 0.0076

Table S317. Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
5P LOSS MUTATED	5	6	0	1	0	4
5P LOSS WILD-TYPE	36	31	39	11	41	20

Figure S317. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S318. Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
5P LOSS MUTATED	47	4	4
5P LOSS WILD-TYPE	187	149	146

Figure S318. 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 = 3e-05

Table S319. 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	33	0	8	1	9	4	0
5P LOSS WILD-TYPE	90	53	39	64	99	62	75

Figure S319. 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 = 3e-05

Table S320. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
5P LOSS MUTATED	43	6	5
5P LOSS WILD-TYPE	180	144	152

Figure S320. 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 = 3e-05

Table S321. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
5P LOSS MUTATED	20	0	2	32
5P LOSS WILD-TYPE	199	58	135	84

Figure S321. 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 = 0.00013

Table S322. Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
5P LOSS MUTATED	30	10	3
5P LOSS WILD-TYPE	142	86	127

Figure S322. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00086 (Fisher's exact test), Q value = 0.0019

Table S323. Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5P LOSS MUTATED	22	3	18
5P LOSS WILD-TYPE	122	112	121

Figure S323. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.024

Table S324. Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
5Q LOSS MUTATED	1	6	0	0
5Q LOSS WILD-TYPE	13	11	12	10

Figure S324. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00999 (Fisher's exact test), Q value = 0.019

Table S325. 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 S325. 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 = 3e-05

Table S326. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
5Q LOSS MUTATED	66	0	2	2	4
5Q LOSS WILD-TYPE	103	305	17	7	33

Figure S326. 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 = 3e-05

Table S327. Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
5Q LOSS MUTATED	54	6	2
5Q LOSS WILD-TYPE	111	83	169

Figure S327. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 0.0012 (Fisher's exact test), Q value = 0.0026

Table S328. Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
5Q LOSS MUTATED	5	7	1	0	0	6
5Q LOSS WILD-TYPE	36	30	38	12	41	18

Figure S328. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0051

Table S329. Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
5Q LOSS MUTATED	11	4	0	4
5Q LOSS WILD-TYPE	56	63	43	13

Figure S329. 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 = 3e-05

Table S330. Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
5Q LOSS MUTATED	65	4	5
5Q LOSS WILD-TYPE	169	149	145

Figure S330. 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 = 3e-05

Table S331. 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	50	0	7	1	11	5	0
5Q LOSS WILD-TYPE	73	53	40	64	97	61	75

Figure S331. 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 = 3e-05

Table S332. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
5Q LOSS MUTATED	61	7	5
5Q LOSS WILD-TYPE	162	143	152

Figure S332. 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 = 3e-05

Table S333. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
5Q LOSS MUTATED	29	0	3	41
5Q LOSS WILD-TYPE	190	58	134	75

Figure S333. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00036

Table S334. Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
5Q LOSS MUTATED	38	14	7
5Q LOSS WILD-TYPE	134	82	123

Figure S334. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S335. Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
5Q LOSS MUTATED	31	4	24
5Q LOSS WILD-TYPE	113	111	115

Figure S335. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.05

Table S336. 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 S336. 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 = 3e-05

Table S337. Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6P LOSS MUTATED	15	0	2	1	0
6P LOSS WILD-TYPE	154	305	17	8	37

Figure S337. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'METHLYATION_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.0028

Table S338. Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
6P LOSS MUTATED	10	2	0
6P LOSS WILD-TYPE	155	87	171

Figure S338. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00088

Table S339. Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
6P LOSS MUTATED	16	1	1
6P LOSS WILD-TYPE	218	152	149

Figure S339. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 5e-04

Table S340. 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	13	1	2	0	2	0	0
6P LOSS WILD-TYPE	110	52	45	65	106	66	75

Figure S340. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.012

Table S341. Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
6P LOSS MUTATED	13	2	1
6P LOSS WILD-TYPE	210	148	156

Figure S341. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00397 (Fisher's exact test), Q value = 0.0079

Table S342. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
6P LOSS MUTATED	8	0	0	8
6P LOSS WILD-TYPE	211	58	137	108

Figure S342. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.043

Table S343. Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
6P LOSS MUTATED	8	0	4
6P LOSS WILD-TYPE	136	115	135

Figure S343. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0301 (Fisher's exact test), Q value = 0.051

Table S344. 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 S344. 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 = 3e-05

Table S345. Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
6Q LOSS MUTATED	22	0	2	1	0
6Q LOSS WILD-TYPE	147	305	17	8	37

Figure S345. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S346. Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
6Q LOSS MUTATED	15	4	0
6Q LOSS WILD-TYPE	150	85	171

Figure S346. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S347. Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
6Q LOSS MUTATED	23	1	1
6Q LOSS WILD-TYPE	211	152	149

Figure S347. 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 = 3e-05

Table S348. 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 S348. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00045

Table S349. Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
6Q LOSS MUTATED	19	3	1
6Q LOSS WILD-TYPE	204	147	156

Figure S349. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S350. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
6Q LOSS MUTATED	10	0	0	13
6Q LOSS WILD-TYPE	209	58	137	103

Figure S350. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.023

Table S351. Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
6Q LOSS MUTATED	13	5	1
6Q LOSS WILD-TYPE	159	91	129

Figure S351. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00358 (Fisher's exact test), Q value = 0.0073

Table S352. Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
6Q LOSS MUTATED	11	0	8
6Q LOSS WILD-TYPE	133	115	131

Figure S352. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p loss' versus 'MRNA_CNMF'

P value = 0.0399 (Fisher's exact test), Q value = 0.065

Table S353. Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
7P LOSS MUTATED	0	4	0	0
7P LOSS WILD-TYPE	14	13	12	10

Figure S353. 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 = 3e-05

Table S354. Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7P LOSS MUTATED	39	3	1	1	0
7P LOSS WILD-TYPE	130	302	18	8	37

Figure S354. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 4e-04 (Fisher's exact test), Q value = 0.00095

Table S355. Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
7P LOSS MUTATED	24	10	5
7P LOSS WILD-TYPE	141	79	166

Figure S355. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.0371 (Fisher's exact test), Q value = 0.061

Table S356. Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
7P LOSS MUTATED	3	4	0	1	0	0
7P LOSS WILD-TYPE	38	33	39	11	41	24

Figure S356. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S357. Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
7P LOSS MUTATED	39	1	4
7P LOSS WILD-TYPE	195	152	146

Figure S357. 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 = 3e-05

Table S358. 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	30	0	2	0	8	4	0
7P LOSS WILD-TYPE	93	53	45	65	100	62	75

Figure S358. 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 = 3e-05

Table S359. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
7P LOSS MUTATED	35	3	6
7P LOSS WILD-TYPE	188	147	151

Figure S359. 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 = 3e-05

Table S360. Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
7P LOSS MUTATED	14	0	3	27
7P LOSS WILD-TYPE	205	58	134	89

Figure S360. 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 = 3e-05

Table S361. Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
7Q LOSS MUTATED	41	0	0	1	0
7Q LOSS WILD-TYPE	128	305	19	8	37

Figure S361. 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 = 3e-05

Table S362. Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
7Q LOSS MUTATED	29	9	1
7Q LOSS WILD-TYPE	136	80	170

Figure S362. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.074

Table S363. Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
7Q LOSS MUTATED	4	4	0	0	0	2
7Q LOSS WILD-TYPE	37	33	39	12	41	22

Figure S363. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.025

Table S364. Gene #55: '7q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
7Q LOSS MUTATED	8	1	0	1
7Q LOSS WILD-TYPE	59	66	43	16

Figure S364. 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 = 3e-05

Table S365. Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
7Q LOSS MUTATED	41	0	1
7Q LOSS WILD-TYPE	193	153	149

Figure S365. 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 = 3e-05

Table S366. 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	32	0	4	0	4	2	0
7Q LOSS WILD-TYPE	91	53	43	65	104	64	75

Figure S366. 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 = 3e-05

Table S367. Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
7Q LOSS MUTATED	38	2	2
7Q LOSS WILD-TYPE	185	148	155

Figure S367. 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 = 3e-05

Table S368. Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
7Q LOSS MUTATED	10	0	1	31
7Q LOSS WILD-TYPE	209	58	136	85

Figure S368. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0055

Table S369. Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
7Q LOSS MUTATED	25	8	4
7Q LOSS WILD-TYPE	147	88	126

Figure S369. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00034 (Fisher's exact test), Q value = 0.00082

Table S370. Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
7Q LOSS MUTATED	22	2	13
7Q LOSS WILD-TYPE	122	113	126

Figure S370. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.015

Table S371. Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
8P LOSS MUTATED	0	5	0	0
8P LOSS WILD-TYPE	14	12	12	10

Figure S371. 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 = 0.00011

Table S372. 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 S372. 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 = 3e-05

Table S373. Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8P LOSS MUTATED	75	3	1	1	0
8P LOSS WILD-TYPE	94	302	18	8	37

Figure S373. 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 = 3e-05

Table S374. Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
8P LOSS MUTATED	58	11	2
8P LOSS WILD-TYPE	107	78	169

Figure S374. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.056

Table S375. Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
8P LOSS MUTATED	5	2	3	0	0	5
8P LOSS WILD-TYPE	36	35	36	12	41	19

Figure S375. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0251 (Fisher's exact test), Q value = 0.043

Table S376. Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
8P LOSS MUTATED	8	4	0	3
8P LOSS WILD-TYPE	59	63	43	14

Figure S376. 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 = 3e-05

Table S377. Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
8P LOSS MUTATED	73	3	3
8P LOSS WILD-TYPE	161	150	147

Figure S377. 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 = 3e-05

Table S378. 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	57	0	11	1	6	3	1
8P LOSS WILD-TYPE	66	53	36	64	102	63	74

Figure S378. 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 = 3e-05

Table S379. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
8P LOSS MUTATED	68	5	4
8P LOSS WILD-TYPE	155	145	153

Figure S379. 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 = 3e-05

Table S380. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
8P LOSS MUTATED	19	0	4	54
8P LOSS WILD-TYPE	200	58	133	62

Figure S380. 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 = 3e-05

Table S381. Gene #56: '8p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
8P LOSS MUTATED	45	15	6
8P LOSS WILD-TYPE	127	81	124

Figure S381. 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 = 3e-05

Table S382. Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
8P LOSS MUTATED	41	3	22
8P LOSS WILD-TYPE	103	112	117

Figure S382. 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 = 3e-05

Table S383. Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
8Q LOSS MUTATED	23	1	1	0	0
8Q LOSS WILD-TYPE	146	304	18	9	37

Figure S383. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S384. Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
8Q LOSS MUTATED	20	3	0
8Q LOSS WILD-TYPE	145	86	171

Figure S384. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S385. Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
8Q LOSS MUTATED	23	0	2
8Q LOSS WILD-TYPE	211	153	148

Figure S385. 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 = 3e-05

Table S386. 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	19	0	3	0	1	1	1
8Q LOSS WILD-TYPE	104	53	44	65	107	65	74

Figure S386. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S387. Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
8Q LOSS MUTATED	21	1	2
8Q LOSS WILD-TYPE	202	149	155

Figure S387. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S388. Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
8Q LOSS MUTATED	6	0	2	16
8Q LOSS WILD-TYPE	213	58	135	100

Figure S388. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0021

Table S389. Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
8Q LOSS MUTATED	17	3	1
8Q LOSS WILD-TYPE	155	93	129

Figure S389. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0087 (Fisher's exact test), Q value = 0.016

Table S390. Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
8Q LOSS MUTATED	13	1	7
8Q LOSS WILD-TYPE	131	114	132

Figure S390. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.0025

Table S391. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9P LOSS MUTATED	1	8	0	0
9P LOSS WILD-TYPE	13	9	12	10

Figure S391. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S392. 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 S392. 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 = 3e-05

Table S393. Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9P LOSS MUTATED	90	2	6	1	4
9P LOSS WILD-TYPE	79	303	13	8	33

Figure S393. 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 = 3e-05

Table S394. Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
9P LOSS MUTATED	59	20	9
9P LOSS WILD-TYPE	106	69	162

Figure S394. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.0076

Table S395. Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
9P LOSS MUTATED	5	9	1	1	1	6
9P LOSS WILD-TYPE	36	28	38	11	40	18

Figure S395. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S396. Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
9P LOSS MUTATED	84	6	13
9P LOSS WILD-TYPE	150	147	137

Figure S396. 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 = 3e-05

Table S397. 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	58	0	18	2	13	11	1
9P LOSS WILD-TYPE	65	53	29	63	95	55	74

Figure S397. 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 = 3e-05

Table S398. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
9P LOSS MUTATED	74	12	14
9P LOSS WILD-TYPE	149	138	143

Figure S398. 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 = 3e-05

Table S399. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
9P LOSS MUTATED	30	1	11	58
9P LOSS WILD-TYPE	189	57	126	58

Figure S399. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0091 (Fisher's exact test), Q value = 0.017

Table S400. Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
9P LOSS MUTATED	47	22	17
9P LOSS WILD-TYPE	125	74	113

Figure S400. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.0014

Table S401. Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
9P LOSS MUTATED	44	13	29
9P LOSS WILD-TYPE	100	102	110

Figure S401. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00011

Table S402. Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
9Q LOSS MUTATED	0	9	0	0
9Q LOSS WILD-TYPE	14	8	12	10

Figure S402. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S403. 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 S403. 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 = 3e-05

Table S404. Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
9Q LOSS MUTATED	105	3	7	2	5
9Q LOSS WILD-TYPE	64	302	12	7	32

Figure S404. 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 = 3e-05

Table S405. Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
9Q LOSS MUTATED	71	22	13
9Q LOSS WILD-TYPE	94	67	158

Figure S405. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.00088

Table S406. Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
9Q LOSS MUTATED	6	12	1	2	1	6
9Q LOSS WILD-TYPE	35	25	38	10	40	18

Figure S406. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S407. Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
9Q LOSS MUTATED	99	8	15
9Q LOSS WILD-TYPE	135	145	135

Figure S407. 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 = 3e-05

Table S408. 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	70	0	18	3	17	13	1
9Q LOSS WILD-TYPE	53	53	29	62	91	53	74

Figure S408. 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 = 3e-05

Table S409. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
9Q LOSS MUTATED	86	17	16
9Q LOSS WILD-TYPE	137	133	141

Figure S409. 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 = 3e-05

Table S410. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
9Q LOSS MUTATED	43	1	12	63
9Q LOSS WILD-TYPE	176	57	125	53

Figure S410. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00111 (Fisher's exact test), Q value = 0.0024

Table S411. Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
9Q LOSS MUTATED	56	28	19
9Q LOSS WILD-TYPE	116	68	111

Figure S411. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00013

Table S412. Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
9Q LOSS MUTATED	55	15	33
9Q LOSS WILD-TYPE	89	100	106

Figure S412. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'MRNA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.064

Table S413. Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
10P LOSS MUTATED	0	4	0	0
10P LOSS WILD-TYPE	14	13	12	10

Figure S413. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0295 (Fisher's exact test), Q value = 0.05

Table S414. 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 S414. 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 = 3e-05

Table S415. Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10P LOSS MUTATED	42	0	1	0	0
10P LOSS WILD-TYPE	127	305	18	9	37

Figure S415. 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 = 3e-05

Table S416. Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
10P LOSS MUTATED	31	5	1
10P LOSS WILD-TYPE	134	84	170

Figure S416. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S417. Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
10P LOSS MUTATED	39	1	3
10P LOSS WILD-TYPE	195	152	147

Figure S417. 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 = 3e-05

Table S418. 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	7	1	4	3	0
10P LOSS WILD-TYPE	95	53	40	64	104	63	75

Figure S418. 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 = 3e-05

Table S419. Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
10P LOSS MUTATED	35	4	2
10P LOSS WILD-TYPE	188	146	155

Figure S419. 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 = 3e-05

Table S420. Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
10P LOSS MUTATED	12	0	2	27
10P LOSS WILD-TYPE	207	58	135	89

Figure S420. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0251 (Fisher's exact test), Q value = 0.043

Table S421. Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
10P LOSS MUTATED	21	10	5
10P LOSS WILD-TYPE	151	86	125

Figure S421. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00406 (Fisher's exact test), Q value = 0.0081

Table S422. Gene #60: '10p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
10P LOSS MUTATED	20	3	13
10P LOSS WILD-TYPE	124	112	126

Figure S422. 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 = 3e-05

Table S423. Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
10Q LOSS MUTATED	38	1	1	0	0
10Q LOSS WILD-TYPE	131	304	18	9	37

Figure S423. 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 = 3e-05

Table S424. Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
10Q LOSS MUTATED	28	6	1
10Q LOSS WILD-TYPE	137	83	170

Figure S424. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S425. Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
10Q LOSS MUTATED	35	1	4
10Q LOSS WILD-TYPE	199	152	146

Figure S425. 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 = 3e-05

Table S426. 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 S426. 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 = 3e-05

Table S427. Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
10Q LOSS MUTATED	32	4	3
10Q LOSS WILD-TYPE	191	146	154

Figure S427. 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 = 3e-05

Table S428. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
10Q LOSS MUTATED	14	0	3	22
10Q LOSS WILD-TYPE	205	58	134	94

Figure S428. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0316 (Fisher's exact test), Q value = 0.053

Table S429. Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
10Q LOSS MUTATED	22	6	6
10Q LOSS WILD-TYPE	150	90	124

Figure S429. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00466 (Fisher's exact test), Q value = 0.0092

Table S430. Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
10Q LOSS MUTATED	21	4	9
10Q LOSS WILD-TYPE	123	111	130

Figure S430. 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 = 3e-05

Table S431. Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11P LOSS MUTATED	66	0	3	4	2
11P LOSS WILD-TYPE	103	305	16	5	35

Figure S431. 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 = 3e-05

Table S432. Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
11P LOSS MUTATED	53	12	5
11P LOSS WILD-TYPE	112	77	166

Figure S432. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S433. Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
11P LOSS MUTATED	65	3	7
11P LOSS WILD-TYPE	169	150	143

Figure S433. 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 = 3e-05

Table S434. 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	7	0
11P LOSS WILD-TYPE	79	52	36	64	97	59	75

Figure S434. 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 = 3e-05

Table S435. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
11P LOSS MUTATED	57	9	8
11P LOSS WILD-TYPE	166	141	149

Figure S435. 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 = 3e-05

Table S436. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
11P LOSS MUTATED	28	0	6	40
11P LOSS WILD-TYPE	191	58	131	76

Figure S436. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.0011

Table S437. Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
11P LOSS MUTATED	44	15	11
11P LOSS WILD-TYPE	128	81	119

Figure S437. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S438. Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
11P LOSS MUTATED	44	8	18
11P LOSS WILD-TYPE	100	107	121

Figure S438. 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 = 3e-05

Table S439. Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
11Q LOSS MUTATED	62	0	4	4	2
11Q LOSS WILD-TYPE	107	305	15	5	35

Figure S439. 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 = 3e-05

Table S440. Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
11Q LOSS MUTATED	52	11	6
11Q LOSS WILD-TYPE	113	78	165

Figure S440. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S441. Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
11Q LOSS MUTATED	60	3	9
11Q LOSS WILD-TYPE	174	150	141

Figure S441. 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 = 3e-05

Table S442. 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	6	0
11Q LOSS WILD-TYPE	79	52	37	64	98	60	75

Figure S442. 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 = 3e-05

Table S443. Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
11Q LOSS MUTATED	55	8	9
11Q LOSS WILD-TYPE	168	142	148

Figure S443. 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 = 3e-05

Table S444. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
11Q LOSS MUTATED	26	0	7	39
11Q LOSS WILD-TYPE	193	58	130	77

Figure S444. 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 = 3e-05

Table S445. Gene #63: '11q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
11Q LOSS MUTATED	49	10	10
11Q LOSS WILD-TYPE	123	86	120

Figure S445. 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 = 3e-05

Table S446. Gene #63: '11q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
11Q LOSS MUTATED	46	8	15
11Q LOSS WILD-TYPE	98	107	124

Figure S446. 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 = 3e-05

Table S447. Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12P LOSS MUTATED	41	0	0	0	2
12P LOSS WILD-TYPE	128	305	19	9	35

Figure S447. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

'12p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S448. Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12P LOSS MUTATED	29	3	4
12P LOSS WILD-TYPE	136	86	167

Figure S448. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 0.0416 (Fisher's exact test), Q value = 0.067

Table S449. Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
12P LOSS MUTATED	2	6	1	0	0	2
12P LOSS WILD-TYPE	39	31	38	12	41	22

Figure S449. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 0.062

Table S450. Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
12P LOSS MUTATED	7	2	0	2
12P LOSS WILD-TYPE	60	65	43	15

Figure S450. 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 = 3e-05

Table S451. Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
12P LOSS MUTATED	38	0	5
12P LOSS WILD-TYPE	196	153	145

Figure S451. 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 = 3e-05

Table S452. 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	27	0	7	1	3	5	0
12P LOSS WILD-TYPE	96	53	40	64	105	61	75

Figure S452. 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 = 3e-05

Table S453. Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
12P LOSS MUTATED	35	2	4
12P LOSS WILD-TYPE	188	148	153

Figure S453. 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 = 3e-05

Table S454. Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
12P LOSS MUTATED	9	0	3	29
12P LOSS WILD-TYPE	210	58	134	87

Figure S454. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00091

Table S455. Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
12P LOSS MUTATED	26	5	4
12P LOSS WILD-TYPE	146	91	126

Figure S455. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0025 (Fisher's exact test), Q value = 0.0052

Table S456. Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
12P LOSS MUTATED	22	4	9
12P LOSS WILD-TYPE	122	111	130

Figure S456. 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 = 3e-05

Table S457. Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
12Q LOSS MUTATED	34	0	0	0	2
12Q LOSS WILD-TYPE	135	305	19	9	35

Figure S457. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

'12q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S458. Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
12Q LOSS MUTATED	27	1	2
12Q LOSS WILD-TYPE	138	88	169

Figure S458. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.028

Table S459. Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
12Q LOSS MUTATED	7	1	0	2
12Q LOSS WILD-TYPE	60	66	43	15

Figure S459. 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 = 3e-05

Table S460. Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
12Q LOSS MUTATED	33	0	3
12Q LOSS WILD-TYPE	201	153	147

Figure S460. 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 = 3e-05

Table S461. 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	25	0	6	0	2	3	0
12Q LOSS WILD-TYPE	98	53	41	65	106	63	75

Figure S461. 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 = 3e-05

Table S462. Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
12Q LOSS MUTATED	29	3	2
12Q LOSS WILD-TYPE	194	147	155

Figure S462. 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 = 3e-05

Table S463. Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
12Q LOSS MUTATED	9	0	1	24
12Q LOSS WILD-TYPE	210	58	136	92

Figure S463. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 8.2e-05

Table S464. Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
12Q LOSS MUTATED	24	3	2
12Q LOSS WILD-TYPE	148	93	128

Figure S464. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S465. Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
12Q LOSS MUTATED	20	2	7
12Q LOSS WILD-TYPE	124	113	132

Figure S465. 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 = 3e-05

Table S466. Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
13Q LOSS MUTATED	71	6	8	3	5
13Q LOSS WILD-TYPE	98	299	11	6	32

Figure S466. 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 = 3e-05

Table S467. Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
13Q LOSS MUTATED	51	17	13
13Q LOSS WILD-TYPE	114	72	158

Figure S467. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.042

Table S468. Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
13Q LOSS MUTATED	4	8	0	1	3	4
13Q LOSS WILD-TYPE	37	29	39	11	38	20

Figure S468. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S469. Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
13Q LOSS MUTATED	68	9	16
13Q LOSS WILD-TYPE	166	144	134

Figure S469. 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 = 3e-05

Table S470. 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	38	4	14	0	24	12	1
13Q LOSS WILD-TYPE	85	49	33	65	84	54	74

Figure S470. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S471. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
13Q LOSS MUTATED	60	18	14
13Q LOSS WILD-TYPE	163	132	143

Figure S471. 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 = 3e-05

Table S472. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
13Q LOSS MUTATED	44	3	11	34
13Q LOSS WILD-TYPE	175	55	126	82

Figure S472. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00203 (Fisher's exact test), Q value = 0.0043

Table S473. Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
13Q LOSS MUTATED	43	16	22
13Q LOSS WILD-TYPE	101	99	117

Figure S473. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 0.0021 (Fisher's exact test), Q value = 0.0044

Table S474. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
14Q LOSS MUTATED	0	6	0	0
14Q LOSS WILD-TYPE	14	11	12	10

Figure S474. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00045 (Fisher's exact test), Q value = 0.0011

Table S475. 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 S475. 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 = 3e-05

Table S476. Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
14Q LOSS MUTATED	54	0	2	3	2
14Q LOSS WILD-TYPE	115	305	17	6	35

Figure S476. 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 = 3e-05

Table S477. Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
14Q LOSS MUTATED	40	7	1
14Q LOSS WILD-TYPE	125	82	170

Figure S477. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.026

Table S478. Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
14Q LOSS MUTATED	5	6	0	0	1	4
14Q LOSS WILD-TYPE	36	31	39	12	40	20

Figure S478. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0499 (Fisher's exact test), Q value = 0.079

Table S479. Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	67	67	43	17
14Q LOSS MUTATED	9	3	1	3
14Q LOSS WILD-TYPE	58	64	42	14

Figure S479. 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 = 3e-05

Table S480. Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
14Q LOSS MUTATED	54	3	4
14Q LOSS WILD-TYPE	180	150	146

Figure S480. 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 = 3e-05

Table S481. 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	45	1	4	0	7	4	0
14Q LOSS WILD-TYPE	78	52	43	65	101	62	75

Figure S481. 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 = 3e-05

Table S482. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
14Q LOSS MUTATED	49	8	2
14Q LOSS WILD-TYPE	174	142	155

Figure S482. 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 = 3e-05

Table S483. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
14Q LOSS MUTATED	20	0	2	37
14Q LOSS WILD-TYPE	199	58	135	79

Figure S483. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.0097

Table S484. Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
14Q LOSS MUTATED	30	10	7
14Q LOSS WILD-TYPE	142	86	123

Figure S484. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S485. Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
14Q LOSS MUTATED	31	3	13
14Q LOSS WILD-TYPE	113	112	126

Figure S485. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.0017

Table S486. Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
15Q LOSS MUTATED	0	7	0	0
15Q LOSS WILD-TYPE	14	10	12	10

Figure S486. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00018

Table S487. 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 S487. 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 = 3e-05

Table S488. Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
15Q LOSS MUTATED	91	4	6	5	3
15Q LOSS WILD-TYPE	78	301	13	4	34

Figure S488. 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 = 3e-05

Table S489. Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
15Q LOSS MUTATED	70	18	8
15Q LOSS WILD-TYPE	95	71	163

Figure S489. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.002

Table S490. Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
15Q LOSS MUTATED	1	11	2	1	1	3
15Q LOSS WILD-TYPE	40	26	37	11	40	21

Figure S490. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S491. Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
15Q LOSS MUTATED	94	6	9
15Q LOSS WILD-TYPE	140	147	141

Figure S491. 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 = 3e-05

Table S492. 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	71	1	9	2	18	7	1
15Q LOSS WILD-TYPE	52	52	38	63	90	59	74

Figure S492. 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 = 3e-05

Table S493. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
15Q LOSS MUTATED	86	13	8
15Q LOSS WILD-TYPE	137	137	149

Figure S493. 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 = 3e-05

Table S494. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
15Q LOSS MUTATED	41	0	5	61
15Q LOSS WILD-TYPE	178	58	132	55

Figure S494. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S495. Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
15Q LOSS MUTATED	58	23	13
15Q LOSS WILD-TYPE	114	73	117

Figure S495. 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 = 3e-05

Table S496. Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
15Q LOSS MUTATED	55	8	31
15Q LOSS WILD-TYPE	89	107	108

Figure S496. 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 = 0.0048

Table S497. Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
16P LOSS MUTATED	0	6	0	0
16P LOSS WILD-TYPE	14	11	12	10

Figure S497. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00767 (Fisher's exact test), Q value = 0.014

Table S498. 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 S498. 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 = 3e-05

Table S499. Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16P LOSS MUTATED	85	4	4	1	3
16P LOSS WILD-TYPE	84	301	15	8	34

Figure S499. 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 = 3e-05

Table S500. Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
16P LOSS MUTATED	61	20	6
16P LOSS WILD-TYPE	104	69	165

Figure S500. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S501. Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
16P LOSS MUTATED	85	4	8
16P LOSS WILD-TYPE	149	149	142

Figure S501. 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 = 3e-05

Table S502. 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	3	11	1	14	7	1
16P LOSS WILD-TYPE	63	50	36	64	94	59	74

Figure S502. 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 = 3e-05

Table S503. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
16P LOSS MUTATED	74	11	9
16P LOSS WILD-TYPE	149	139	148

Figure S503. 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 = 3e-05

Table S504. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
16P LOSS MUTATED	34	1	6	53
16P LOSS WILD-TYPE	185	57	131	63

Figure S504. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00416 (Fisher's exact test), Q value = 0.0083

Table S505. Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
16P LOSS MUTATED	47	23	16
16P LOSS WILD-TYPE	125	73	114

Figure S505. 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 = 3e-05

Table S506. Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
16P LOSS MUTATED	46	7	33
16P LOSS WILD-TYPE	98	108	106

Figure S506. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q loss' versus 'MRNA_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0018

Table S507. Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
16Q LOSS MUTATED	0	8	1	0
16Q LOSS WILD-TYPE	14	9	11	10

Figure S507. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00135 (Fisher's exact test), Q value = 0.0029

Table S508. 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 S508. 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 = 3e-05

Table S509. Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
16Q LOSS MUTATED	112	14	7	1	4
16Q LOSS WILD-TYPE	57	291	12	8	33

Figure S509. 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 = 3e-05

Table S510. Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
16Q LOSS MUTATED	80	26	15
16Q LOSS WILD-TYPE	85	63	156

Figure S510. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S511. Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
16Q LOSS MUTATED	110	14	14
16Q LOSS WILD-TYPE	124	139	136

Figure S511. 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 = 3e-05

Table S512. 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	78	7	16	3	21	9	4
16Q LOSS WILD-TYPE	45	46	31	62	87	57	71

Figure S512. 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 = 3e-05

Table S513. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
16Q LOSS MUTATED	96	23	15
16Q LOSS WILD-TYPE	127	127	142

Figure S513. 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 = 3e-05

Table S514. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
16Q LOSS MUTATED	49	6	12	67
16Q LOSS WILD-TYPE	170	52	125	49

Figure S514. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00064

Table S515. Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
16Q LOSS MUTATED	66	30	22
16Q LOSS WILD-TYPE	106	66	108

Figure S515. 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 = 3e-05

Table S516. Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
16Q LOSS MUTATED	61	13	44
16Q LOSS WILD-TYPE	83	102	95

Figure S516. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.0067

Table S517. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
17P LOSS MUTATED	0	7	1	0
17P LOSS WILD-TYPE	14	10	11	10

Figure S517. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00036

Table S518. 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 S518. 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 = 3e-05

Table S519. Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17P LOSS MUTATED	120	3	4	1	2
17P LOSS WILD-TYPE	49	302	15	8	35

Figure S519. 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 = 3e-05

Table S520. Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
17P LOSS MUTATED	83	21	11
17P LOSS WILD-TYPE	82	68	160

Figure S520. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 0.00361 (Fisher's exact test), Q value = 0.0073

Table S521. Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
17P LOSS MUTATED	5	8	3	0	1	8
17P LOSS WILD-TYPE	36	29	36	12	40	16

Figure S521. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S522. Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
17P LOSS MUTATED	110	4	15
17P LOSS WILD-TYPE	124	149	135

Figure S522. 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 = 3e-05

Table S523. 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	84	1	10	3	17	13	1
17P LOSS WILD-TYPE	39	52	37	62	91	53	74

Figure S523. 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 = 3e-05

Table S524. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
17P LOSS MUTATED	99	12	16
17P LOSS WILD-TYPE	124	138	141

Figure S524. 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 = 3e-05

Table S525. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
17P LOSS MUTATED	45	0	13	69
17P LOSS WILD-TYPE	174	58	124	47

Figure S525. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S526. Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
17P LOSS MUTATED	66	28	16
17P LOSS WILD-TYPE	106	68	114

Figure S526. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S527. Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
17P LOSS MUTATED	59	16	35
17P LOSS WILD-TYPE	85	99	104

Figure S527. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 0.00199 (Fisher's exact test), Q value = 0.0042

Table S528. Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
17Q LOSS MUTATED	0	6	0	0
17Q LOSS WILD-TYPE	14	11	12	10

Figure S528. 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 = 5.6e-05

Table S529. 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 S529. 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 = 3e-05

Table S530. Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
17Q LOSS MUTATED	84	2	4	1	2
17Q LOSS WILD-TYPE	85	303	15	8	35

Figure S530. 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 = 3e-05

Table S531. Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
17Q LOSS MUTATED	54	18	10
17Q LOSS WILD-TYPE	111	71	161

Figure S531. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S532. Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
17Q LOSS MUTATED	75	4	13
17Q LOSS WILD-TYPE	159	149	137

Figure S532. 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 = 3e-05

Table S533. 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 S533. 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 = 3e-05

Table S534. Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
17Q LOSS MUTATED	66	10	14
17Q LOSS WILD-TYPE	157	140	143

Figure S534. 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 = 3e-05

Table S535. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
17Q LOSS MUTATED	34	0	11	45
17Q LOSS WILD-TYPE	185	58	126	71

Figure S535. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00417 (Fisher's exact test), Q value = 0.0083

Table S536. Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
17Q LOSS MUTATED	46	19	15
17Q LOSS WILD-TYPE	126	77	115

Figure S536. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0012

Table S537. Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
17Q LOSS MUTATED	44	14	22
17Q LOSS WILD-TYPE	100	101	117

Figure S537. 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 = 3e-05

Table S538. Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18P LOSS MUTATED	38	1	6	4	3
18P LOSS WILD-TYPE	131	304	13	5	34

Figure S538. 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 = 3e-05

Table S539. Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18P LOSS MUTATED	34	8	4
18P LOSS WILD-TYPE	131	81	167

Figure S539. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S540. Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
18P LOSS MUTATED	40	5	7
18P LOSS WILD-TYPE	194	148	143

Figure S540. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S541. 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	17	6	0
18P LOSS WILD-TYPE	102	52	41	64	91	60	75

Figure S541. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.00026

Table S542. Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
18P LOSS MUTATED	36	8	7
18P LOSS WILD-TYPE	187	142	150

Figure S542. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00021

Table S543. Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
18P LOSS MUTATED	24	1	5	21
18P LOSS WILD-TYPE	195	57	132	95

Figure S543. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.031

Table S544. Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
18P LOSS MUTATED	29	8	9
18P LOSS WILD-TYPE	143	88	121

Figure S544. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00361 (Fisher's exact test), Q value = 0.0073

Table S545. Gene #73: '18p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
18P LOSS MUTATED	27	7	12
18P LOSS WILD-TYPE	117	108	127

Figure S545. 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 = 3e-05

Table S546. Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
18Q LOSS MUTATED	50	1	7	4	3
18Q LOSS WILD-TYPE	119	304	12	5	34

Figure S546. 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 = 3e-05

Table S547. Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
18Q LOSS MUTATED	42	11	6
18Q LOSS WILD-TYPE	123	78	165

Figure S547. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S548. Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
18Q LOSS MUTATED	52	5	8
18Q LOSS WILD-TYPE	182	148	142

Figure S548. 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 = 3e-05

Table S549. 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	27	1	11	1	19	6	0
18Q LOSS WILD-TYPE	96	52	36	64	89	60	75

Figure S549. 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 = 3e-05

Table S550. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
18Q LOSS MUTATED	48	7	9
18Q LOSS WILD-TYPE	175	143	148

Figure S550. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S551. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
18Q LOSS MUTATED	25	0	6	33
18Q LOSS WILD-TYPE	194	58	131	83

Figure S551. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.021

Table S552. Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
18Q LOSS MUTATED	36	11	12
18Q LOSS WILD-TYPE	136	85	118

Figure S552. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.00097

Table S553. Gene #74: '18q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
18Q LOSS MUTATED	34	8	17
18Q LOSS WILD-TYPE	110	107	122

Figure S553. 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 = 3e-05

Table S554. Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19P LOSS MUTATED	51	0	5	2	1
19P LOSS WILD-TYPE	118	305	14	7	36

Figure S554. 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 = 3e-05

Table S555. Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19P LOSS MUTATED	45	6	2
19P LOSS WILD-TYPE	120	83	169

Figure S555. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S556. Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
19P LOSS MUTATED	50	4	5
19P LOSS WILD-TYPE	184	149	145

Figure S556. 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 = 3e-05

Table S557. 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	9	1	11	3	0
19P LOSS WILD-TYPE	89	52	38	64	97	63	75

Figure S557. 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 = 3e-05

Table S558. Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
19P LOSS MUTATED	44	7	6
19P LOSS WILD-TYPE	179	143	151

Figure S558. 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 = 3e-05

Table S559. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
19P LOSS MUTATED	23	0	3	31
19P LOSS WILD-TYPE	196	58	134	85

Figure S559. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00523 (Fisher's exact test), Q value = 0.01

Table S560. Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
19P LOSS MUTATED	33	8	10
19P LOSS WILD-TYPE	139	88	120

Figure S560. 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 = 3e-05

Table S561. Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
19P LOSS MUTATED	37	3	11
19P LOSS WILD-TYPE	107	112	128

Figure S561. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.03

Table S562. Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	14	9	7	7	16
19Q LOSS MUTATED	0	3	1	0	0
19Q LOSS WILD-TYPE	14	6	6	7	16

Figure S562. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S563. Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
19Q LOSS MUTATED	49	1	4	1	1
19Q LOSS WILD-TYPE	120	304	15	8	36

Figure S563. 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 = 3e-05

Table S564. Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
19Q LOSS MUTATED	37	8	4
19Q LOSS WILD-TYPE	128	81	167

Figure S564. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S565. Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
19Q LOSS MUTATED	45	4	6
19Q LOSS WILD-TYPE	189	149	144

Figure S565. 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 = 3e-05

Table S566. 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	6	1	9	4	0
19Q LOSS WILD-TYPE	89	52	41	64	99	62	75

Figure S566. 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 = 3e-05

Table S567. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
19Q LOSS MUTATED	41	6	7
19Q LOSS WILD-TYPE	182	144	150

Figure S567. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S568. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
19Q LOSS MUTATED	25	0	4	25
19Q LOSS WILD-TYPE	194	58	133	91

Figure S568. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.021

Table S569. Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
19Q LOSS MUTATED	30	8	9
19Q LOSS WILD-TYPE	142	88	121

Figure S569. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S570. Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
19Q LOSS MUTATED	31	4	12
19Q LOSS WILD-TYPE	113	111	127

Figure S570. 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 = 3e-05

Table S571. Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20P LOSS MUTATED	16	1	1	1	0
20P LOSS WILD-TYPE	153	304	18	8	37

Figure S571. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.029

Table S572. Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
20P LOSS MUTATED	14	2	2
20P LOSS WILD-TYPE	220	151	148

Figure S572. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.019

Table S573. 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	10	2	3	0	2	1	0
20P LOSS WILD-TYPE	113	51	44	65	106	65	75

Figure S573. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 0.00707 (Fisher's exact test), Q value = 0.013

Table S574. Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
20P LOSS MUTATED	14	3	1
20P LOSS WILD-TYPE	209	147	156

Figure S574. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0012

Table S575. Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
20Q LOSS MUTATED	7	0	1	1	0
20Q LOSS WILD-TYPE	162	305	18	8	37

Figure S575. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.061

Table S576. Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
20Q LOSS MUTATED	7	1	0
20Q LOSS WILD-TYPE	227	152	150

Figure S576. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0307 (Fisher's exact test), Q value = 0.052

Table S577. Gene #78: '20q 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
20Q LOSS MUTATED	5	1	2	0	0	0	0
20Q LOSS WILD-TYPE	118	52	45	65	108	66	75

Figure S577. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.066

Table S578. Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
20Q LOSS MUTATED	7	2	0
20Q LOSS WILD-TYPE	216	148	157

Figure S578. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.075

Table S579. Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
20Q LOSS MUTATED	4	0	0	5
20Q LOSS WILD-TYPE	215	58	137	111

Figure S579. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.065

Table S580. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
21Q LOSS MUTATED	0	4	0	0
21Q LOSS WILD-TYPE	14	13	12	10

Figure S580. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0299 (Fisher's exact test), Q value = 0.051

Table S581. 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 S581. 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 = 3e-05

Table S582. Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
21Q LOSS MUTATED	44	4	2	4	0
21Q LOSS WILD-TYPE	125	301	17	5	37

Figure S582. 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 = 3e-05

Table S583. Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
21Q LOSS MUTATED	34	7	5
21Q LOSS WILD-TYPE	131	82	166

Figure S583. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S584. Gene #79: '21q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
21Q LOSS MUTATED	46	7	1
21Q LOSS WILD-TYPE	188	146	149

Figure S584. 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 = 3e-05

Table S585. 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 S585. 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 = 3e-05

Table S586. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
21Q LOSS MUTATED	43	7	2
21Q LOSS WILD-TYPE	180	143	155

Figure S586. 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 = 3e-05

Table S587. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
21Q LOSS MUTATED	21	1	1	29
21Q LOSS WILD-TYPE	198	57	136	87

Figure S587. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00364 (Fisher's exact test), Q value = 0.0074

Table S588. Gene #79: '21q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
21Q LOSS MUTATED	30	9	7
21Q LOSS WILD-TYPE	142	87	123

Figure S588. 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 = 5.6e-05

Table S589. Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
21Q LOSS MUTATED	28	1	17
21Q LOSS WILD-TYPE	116	114	122

Figure S589. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0042

Table S590. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
22Q LOSS MUTATED	0	6	0	0
22Q LOSS WILD-TYPE	14	11	12	10

Figure S590. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00759 (Fisher's exact test), Q value = 0.014

Table S591. 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 S591. 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 = 3e-05

Table S592. Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
22Q LOSS MUTATED	96	3	4	3	3
22Q LOSS WILD-TYPE	73	302	15	6	34

Figure S592. 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 = 3e-05

Table S593. Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
22Q LOSS MUTATED	67	20	13
22Q LOSS WILD-TYPE	98	69	158

Figure S593. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q loss' versus 'RPPA_CNMF'

P value = 0.0388 (Fisher's exact test), Q value = 0.064

Table S594. Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
22Q LOSS MUTATED	4	8	2	1	1	5
22Q LOSS WILD-TYPE	37	29	37	11	40	19

Figure S594. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S595. Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
22Q LOSS MUTATED	85	6	17
22Q LOSS WILD-TYPE	149	147	133

Figure S595. 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 = 3e-05

Table S596. 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	62	1	7	1	22	13	2
22Q LOSS WILD-TYPE	61	52	40	64	86	53	73

Figure S596. 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 = 3e-05

Table S597. Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
22Q LOSS MUTATED	79	11	17
22Q LOSS WILD-TYPE	144	139	140

Figure S597. 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 = 3e-05

Table S598. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
22Q LOSS MUTATED	43	0	13	51
22Q LOSS WILD-TYPE	176	58	124	65

Figure S598. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00382 (Fisher's exact test), Q value = 0.0077

Table S599. Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
22Q LOSS MUTATED	51	25	18
22Q LOSS WILD-TYPE	121	71	112

Figure S599. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00033

Table S600. Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
22Q LOSS MUTATED	50	15	29
22Q LOSS WILD-TYPE	94	100	110

Figure S600. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp loss' versus 'MRNA_CNMF'

P value = 0.00164 (Fisher's exact test), Q value = 0.0035

Table S601. Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
XP LOSS MUTATED	0	6	0	0
XP LOSS WILD-TYPE	14	11	12	10

Figure S601. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 4e-04 (Fisher's exact test), Q value = 0.00095

Table S602. 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	1	5	0	0	0
XP LOSS WILD-TYPE	13	4	7	7	16

Figure S602. 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 = 3e-05

Table S603. Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
XP LOSS MUTATED	76	1	3	2	3
XP LOSS WILD-TYPE	93	304	16	7	34

Figure S603. 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 = 3e-05

Table S604. Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
XP LOSS MUTATED	46	16	8
XP LOSS WILD-TYPE	119	73	163

Figure S604. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 5.6e-05

Table S605. Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
XP LOSS MUTATED	2	14	2	1	1	2
XP LOSS WILD-TYPE	39	23	37	11	40	22

Figure S605. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S606. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
XP LOSS MUTATED	73	5	6
XP LOSS WILD-TYPE	161	148	144

Figure S606. 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 = 3e-05

Table S607. 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	52	2	6	1	19	4	0
XP LOSS WILD-TYPE	71	51	41	64	89	62	75

Figure S607. 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 = 3e-05

Table S608. Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
XP LOSS MUTATED	61	12	9
XP LOSS WILD-TYPE	162	138	148

Figure S608. 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 = 3e-05

Table S609. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
XP LOSS MUTATED	34	0	4	44
XP LOSS WILD-TYPE	185	58	133	72

Figure S609. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0015

Table S610. Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
XP LOSS MUTATED	44	13	12
XP LOSS WILD-TYPE	128	83	118

Figure S610. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S611. Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
XP LOSS MUTATED	43	6	20
XP LOSS WILD-TYPE	101	109	119

Figure S611. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.00831 (Fisher's exact test), Q value = 0.016

Table S612. Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	14	17	12	10
XQ LOSS MUTATED	0	5	0	0
XQ LOSS WILD-TYPE	14	12	12	10

Figure S612. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0047 (Fisher's exact test), Q value = 0.0092

Table S613. 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	1	4	0	0	0
XQ LOSS WILD-TYPE	13	5	7	7	16

Figure S613. 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 = 3e-05

Table S614. Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	169	305	19	9	37
XQ LOSS MUTATED	64	1	3	2	1
XQ LOSS WILD-TYPE	105	304	16	7	36

Figure S614. 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 = 3e-05

Table S615. Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	165	89	171
XQ LOSS MUTATED	42	12	6
XQ LOSS WILD-TYPE	123	77	165

Figure S615. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 5e-04

Table S616. Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	41	37	39	12	41	24
XQ LOSS MUTATED	3	13	2	1	1	1
XQ LOSS WILD-TYPE	38	24	37	11	40	23

Figure S616. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 3e-05

Table S617. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	234	153	150
XQ LOSS MUTATED	61	4	5
XQ LOSS WILD-TYPE	173	149	145

Figure S617. 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 = 3e-05

Table S618. 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	8	1	15	4	0
XQ LOSS WILD-TYPE	83	51	39	64	93	62	75

Figure S618. 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 = 3e-05

Table S619. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	223	150	157
XQ LOSS MUTATED	51	9	8
XQ LOSS WILD-TYPE	172	141	149

Figure S619. 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 = 3e-05

Table S620. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	219	58	137	116
XQ LOSS MUTATED	26	0	4	38
XQ LOSS WILD-TYPE	193	58	133	78

Figure S620. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00576 (Fisher's exact test), Q value = 0.011

Table S621. Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	172	96	130
XQ LOSS MUTATED	37	9	13
XQ LOSS WILD-TYPE	135	87	117

Figure S621. 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 = 3e-05

Table S622. Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	144	115	139
XQ LOSS MUTATED	41	4	14
XQ LOSS WILD-TYPE	103	111	125

Figure S622. 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/15106276/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UCEC-TP/15120652/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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