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 1080 patients, 810 significant findings detected with P value < 0.05 and Q value < 0.25.

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

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 810 significant findings detected.


		Clinical Features	MRNA CNMF	MRNA CHIERARCHICAL	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
1p gain	227 (21%)	853	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00107 (0.00177)
2p gain	122 (11%)	958	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)
2q gain	73 (7%)	1007	1e-05 (2.35e-05)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00835 (0.0116)
3q gain	213 (20%)	867	0.00515 (0.00745)	0.0121 (0.0163)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	9e-05 (0.000178)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00049 (0.000867)
6p gain	208 (19%)	872	1e-05 (2.35e-05)	0.0002 (0.000371)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
6q gain	149 (14%)	931	1e-05 (2.35e-05)	0.00119 (0.00195)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
8q gain	530 (49%)	550	0.00564 (0.00811)	0.0392 (0.0482)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0105 (0.0143)	0.00078 (0.00132)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
9p gain	139 (13%)	941	0.00022 (0.000405)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00016 (0.000303)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00013 (0.000252)	1e-05 (2.35e-05)	0.00066 (0.00114)	0.049 (0.0595)
10p gain	208 (19%)	872	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
12p gain	225 (21%)	855	0.00016 (0.000303)	0.0249 (0.0316)	1e-05 (2.35e-05)	6e-05 (0.000122)	0.00332 (0.00501)	0.0116 (0.0157)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	6e-05 (0.000122)	0.00465 (0.00679)	0.00398 (0.00591)
16p gain	462 (43%)	618	0.00336 (0.00502)	0.0102 (0.014)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00471 (0.00687)	0.00123 (0.00201)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00051 (0.000898)	1e-05 (2.35e-05)	6e-05 (0.000122)	0.00695 (0.00981)
18p gain	177 (16%)	903	0.00016 (0.000303)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
18q gain	154 (14%)	926	0.00285 (0.00437)	4e-05 (8.36e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00196 (0.00312)	0.00633 (0.00904)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00015 (0.000287)	0.00483 (0.00703)
21q gain	198 (18%)	882	1e-05 (2.35e-05)	0.00054 (0.000942)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
22q gain	99 (9%)	981	1e-05 (2.35e-05)	0.0079 (0.011)	1e-05 (2.35e-05)	4e-05 (8.36e-05)	4e-05 (8.36e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	7e-05 (0.000141)	0.00391 (0.00581)
xq gain	137 (13%)	943	0.00453 (0.00663)	0.00677 (0.00961)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0173 (0.0226)	0.00049 (0.000867)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00014 (0.00027)	7e-05 (0.000141)	0.00423 (0.00624)
3p loss	188 (17%)	892	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	4e-05 (8.36e-05)	0.0158 (0.0209)
4p loss	353 (33%)	727	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
4q loss	311 (29%)	769	1e-05 (2.35e-05)	0.00015 (0.000287)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00022 (0.000405)
5p loss	142 (13%)	938	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
5q loss	228 (21%)	852	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
9q loss	280 (26%)	800	1e-05 (2.35e-05)	0.0217 (0.0278)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	9e-05 (0.000178)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
10q loss	231 (21%)	849	0.00011 (0.000216)	0.014 (0.0187)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0053 (0.00766)	0.00079 (0.00133)
12p loss	153 (14%)	927	0.00017 (0.000321)	0.00165 (0.00266)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	4e-05 (8.36e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
12q loss	137 (13%)	943	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
14q loss	269 (25%)	811	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
15q loss	318 (29%)	762	0.0007 (0.0012)	0.00021 (0.000388)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
17q loss	272 (25%)	808	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	0.0134 (0.0179)
20p loss	93 (9%)	987	0.0299 (0.0372)	0.00713 (0.01)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00042 (0.000751)	0.00019 (0.000354)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	9e-05 (0.000178)	0.00126 (0.00206)
xp loss	192 (18%)	888	0.0196 (0.0252)	0.0195 (0.0251)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00019 (0.000354)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00081 (0.00136)	0.00137 (0.00223)	0.00101 (0.00167)
5q gain	211 (20%)	869	0.0182 (0.0235)	0.00353 (0.00526)	1e-05 (2.35e-05)	0.0018 (0.00288)	0.00302 (0.00461)	0.00024 (0.000439)	0.00647 (0.00923)	0.00025 (0.000455)	0.0157 (0.0209)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	0.0656 (0.0784)
7q gain	268 (25%)	812	0.0129 (0.0174)	0.00869 (0.012)	1e-05 (2.35e-05)	0.00026 (0.000471)	0.0454 (0.0555)	0.00231 (0.00363)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	0.00293 (0.00449)	0.188 (0.208)
10q gain	114 (11%)	966	0.00307 (0.00468)	0.0415 (0.0509)	1e-05 (2.35e-05)	0.00054 (0.000942)	0.0106 (0.0144)	0.0643 (0.0769)	0.00073 (0.00124)	7e-05 (0.000141)	0.00021 (0.000388)	3e-05 (6.45e-05)	0.00266 (0.00412)	0.0256 (0.0323)
11q gain	96 (9%)	984	0.0346 (0.0428)	0.0916 (0.107)	1e-05 (2.35e-05)	0.00112 (0.00184)	0.00145 (0.00235)	0.00081 (0.00136)	0.00038 (0.000686)	0.0005 (0.000882)	5e-05 (0.000103)	0.00272 (0.0042)	0.0298 (0.0372)	0.0115 (0.0156)
19p gain	187 (17%)	893	0.00069 (0.00118)	0.0033 (0.00499)	1e-05 (2.35e-05)	0.00025 (0.000455)	0.00237 (0.0037)	0.00418 (0.00619)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	0.00026 (0.000471)	4e-05 (8.36e-05)	4e-05 (8.36e-05)	0.659 (0.67)
19q gain	219 (20%)	861	0.00233 (0.00366)	0.00745 (0.0105)	1e-05 (2.35e-05)	4e-05 (8.36e-05)	0.0157 (0.0209)	0.0164 (0.0215)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	0.00015 (0.000287)	2e-05 (4.45e-05)	0.00045 (0.000804)	0.177 (0.197)
20p gain	411 (38%)	669	0.00015 (0.000287)	0.508 (0.526)	1e-05 (2.35e-05)	0.00185 (0.00295)	0.0132 (0.0178)	0.00463 (0.00677)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00858 (0.0119)	0.00312 (0.00474)
xp gain	150 (14%)	930	0.0198 (0.0254)	0.57 (0.583)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	0.00899 (0.0124)	0.00833 (0.0116)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	6e-05 (0.000122)	5e-05 (0.000103)	0.00012 (0.000234)
2p loss	185 (17%)	895	0.00625 (0.00895)	0.029 (0.0362)	1e-05 (2.35e-05)	9e-05 (0.000178)	0.0299 (0.0372)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	0.00039 (0.000703)	0.0011 (0.00181)	0.0593 (0.0711)
7p loss	111 (10%)	969	0.00559 (0.00805)	0.881 (0.883)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	0.00018 (0.000337)	0.00737 (0.0104)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	4e-05 (8.36e-05)	1e-05 (2.35e-05)	0.00243 (0.00378)
9p loss	313 (29%)	767	5e-05 (0.000103)	0.0402 (0.0494)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	5e-05 (0.000103)	0.192 (0.211)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00014 (0.00027)	1e-05 (2.35e-05)
13q loss	430 (40%)	650	0.0015 (0.00243)	0.0664 (0.0789)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00435 (0.00639)	0.00047 (0.000835)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00052 (0.000912)	0.00067 (0.00115)
16q loss	591 (55%)	489	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00011 (0.000216)	0.0628 (0.0753)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0011 (0.00181)	3e-05 (6.45e-05)
19p loss	197 (18%)	883	0.00016 (0.000303)	0.366 (0.386)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00023 (0.000421)	8e-05 (0.00016)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)
19q loss	164 (15%)	916	0.0129 (0.0174)	0.175 (0.195)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00542 (0.00782)	0.00231 (0.00363)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	0.00013 (0.000252)	2e-05 (4.45e-05)
20q loss	57 (5%)	1023	0.475 (0.493)	0.00078 (0.00132)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00067 (0.00115)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00234 (0.00366)
xq loss	189 (18%)	891	0.0338 (0.0419)	0.872 (0.875)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	0.00421 (0.00622)	0.00056 (0.000975)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	3e-05 (6.45e-05)	0.00241 (0.00375)	0.0106 (0.0144)	0.00283 (0.00436)
17q gain	221 (20%)	859	0.0554 (0.0669)	0.0113 (0.0154)	1e-05 (2.35e-05)	0.00042 (0.000751)	0.51 (0.528)	4e-05 (8.36e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00154 (0.00249)	0.00649 (0.00924)
1p loss	227 (21%)	853	0.0231 (0.0294)	0.0019 (0.00303)	1e-05 (2.35e-05)	0.0005 (0.000882)	0.0982 (0.114)	0.0161 (0.0212)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00329 (0.00498)	1e-05 (2.35e-05)	0.0166 (0.0217)	0.744 (0.75)
3q loss	105 (10%)	975	1e-05 (2.35e-05)	0.0086 (0.0119)	1e-05 (2.35e-05)	4e-05 (8.36e-05)	3e-05 (6.45e-05)	0.00058 (0.00101)	4e-05 (8.36e-05)	7e-05 (0.000141)	0.00203 (0.00322)	0.0002 (0.000371)	0.148 (0.166)	0.0899 (0.105)
8p loss	395 (37%)	685	0.0201 (0.0258)	0.196 (0.215)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00018 (0.000337)	0.0323 (0.04)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	0.0953 (0.111)	0.00237 (0.0037)
11p loss	270 (25%)	810	0.333 (0.353)	0.339 (0.36)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00316 (0.00479)	0.00333 (0.00502)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	2e-05 (4.45e-05)	0.0179 (0.0232)	0.0247 (0.0313)
17p loss	580 (54%)	500	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.241 (0.261)	0.313 (0.333)
18p loss	320 (30%)	760	0.00207 (0.00328)	0.0219 (0.028)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00209 (0.00331)	0.027 (0.0339)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.0147 (0.0196)	1e-05 (2.35e-05)	0.378 (0.398)	0.802 (0.806)
18q loss	321 (30%)	759	0.00093 (0.00155)	0.0042 (0.00621)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00063 (0.00109)	0.00341 (0.00509)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00429 (0.00632)	1e-05 (2.35e-05)	0.27 (0.29)	0.35 (0.371)
4q gain	71 (7%)	1009	0.124 (0.141)	0.00491 (0.00712)	1e-05 (2.35e-05)	0.0162 (0.0213)	0.0212 (0.0272)	0.0284 (0.0355)	0.0001 (0.000197)	0.107 (0.122)	0.0176 (0.0228)	0.0423 (0.0518)	0.518 (0.534)	0.0394 (0.0485)
11p gain	141 (13%)	939	0.128 (0.144)	0.392 (0.411)	1e-05 (2.35e-05)	0.00437 (0.00641)	0.0455 (0.0555)	0.512 (0.529)	0.00019 (0.000354)	0.00843 (0.0117)	0.00011 (0.000216)	3e-05 (6.45e-05)	0.00212 (0.00335)	1e-05 (2.35e-05)
20q gain	450 (42%)	630	9e-05 (0.000178)	0.203 (0.222)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.122 (0.139)	0.106 (0.121)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00062 (0.00107)	3e-05 (6.45e-05)
6q loss	280 (26%)	800	0.202 (0.221)	0.0256 (0.0323)	1e-05 (2.35e-05)	0.00094 (0.00157)	0.712 (0.72)	0.00079 (0.00133)	2e-05 (4.45e-05)	0.00037 (0.000669)	0.00786 (0.011)	2e-05 (4.45e-05)	0.0105 (0.0143)	0.205 (0.223)
7q loss	120 (11%)	960	0.0658 (0.0784)	0.0767 (0.0906)	2e-05 (4.45e-05)	0.00334 (0.00502)	0.0266 (0.0333)	0.376 (0.396)	0.00171 (0.00275)	0.00023 (0.000421)	0.00073 (0.00124)	0.00015 (0.000287)	0.00968 (0.0133)	0.0169 (0.0221)
16p loss	174 (16%)	906	0.0929 (0.108)	0.201 (0.22)	0.00336 (0.00502)	0.00041 (0.000736)	0.00046 (0.00082)	0.00247 (0.00383)	0.00023 (0.000421)	0.00225 (0.00355)	0.00012 (0.000234)	0.00434 (0.00638)	3e-05 (6.45e-05)	0.0661 (0.0787)
3p gain	137 (13%)	943	0.457 (0.476)	0.297 (0.318)	1e-05 (2.35e-05)	5e-05 (0.000103)	0.0255 (0.0323)	0.00774 (0.0108)	2e-05 (4.45e-05)	1e-05 (2.35e-05)	2e-05 (4.45e-05)	6e-05 (0.000122)	0.261 (0.282)	0.178 (0.198)
4p gain	75 (7%)	1005	0.258 (0.278)	0.0158 (0.0209)	1e-05 (2.35e-05)	0.00752 (0.0105)	0.00162 (0.00261)	0.0701 (0.0831)	6e-05 (0.000122)	0.0162 (0.0213)	0.00696 (0.00981)	0.0172 (0.0225)	0.559 (0.573)	0.121 (0.138)
8p gain	291 (27%)	789	0.0658 (0.0784)	0.031 (0.0385)	1e-05 (2.35e-05)	0.00095 (0.00158)	0.429 (0.448)	0.0973 (0.113)	0.00053 (0.000928)	0.00138 (0.00224)	0.0266 (0.0334)	0.0386 (0.0477)	0.0185 (0.0239)	0.0832 (0.0978)
12q gain	186 (17%)	894	0.00063 (0.00109)	0.141 (0.158)	1e-05 (2.35e-05)	0.00185 (0.00295)	0.247 (0.268)	0.026 (0.0327)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.00052 (0.000912)	0.00234 (0.00366)	0.119 (0.135)	0.45 (0.47)
13q gain	93 (9%)	987	0.165 (0.184)	0.604 (0.618)	0.00142 (0.00231)	0.00091 (0.00152)	0.00599 (0.0086)	0.00246 (0.00382)	0.00604 (0.00866)	0.00018 (0.000337)	0.00844 (0.0117)	0.00013 (0.000252)	0.239 (0.26)	0.0632 (0.0757)
14q gain	143 (13%)	937	0.641 (0.653)	0.019 (0.0245)	1e-05 (2.35e-05)	0.00047 (0.000835)	0.0793 (0.0934)	0.0233 (0.0296)	5e-05 (0.000103)	7e-05 (0.000141)	0.00066 (0.00114)	3e-05 (6.45e-05)	0.19 (0.209)	0.308 (0.329)
2q loss	211 (20%)	869	0.106 (0.122)	0.528 (0.543)	1e-05 (2.35e-05)	0.00335 (0.00502)	0.0669 (0.0794)	9e-05 (0.000178)	0.00041 (0.000736)	1e-05 (2.35e-05)	0.00096 (0.00159)	0.0197 (0.0254)	0.00489 (0.0071)	0.0888 (0.104)
22q loss	482 (45%)	598	0.0181 (0.0235)	0.327 (0.348)	1e-05 (2.35e-05)	0.189 (0.208)	0.184 (0.204)	0.00018 (0.000337)	0.0133 (0.0179)	4e-05 (8.36e-05)	0.00375 (0.00558)	0.026 (0.0327)	0.0369 (0.0456)	0.272 (0.292)
5p gain	315 (29%)	765	0.238 (0.258)	0.0402 (0.0494)	1e-05 (2.35e-05)	0.011 (0.0149)	0.523 (0.538)	0.686 (0.694)	0.11 (0.126)	0.0536 (0.0648)	0.0119 (0.0161)	0.0138 (0.0185)	0.0164 (0.0215)	0.302 (0.323)
7p gain	313 (29%)	767	0.122 (0.139)	0.204 (0.223)	1e-05 (2.35e-05)	0.0001 (0.000197)	0.148 (0.166)	0.117 (0.134)	1e-05 (2.35e-05)	3e-05 (6.45e-05)	0.00084 (0.00141)	0.00284 (0.00437)	0.0786 (0.0927)	0.257 (0.277)
9q gain	122 (11%)	958	0.635 (0.647)	0.139 (0.156)	1e-05 (2.35e-05)	0.00104 (0.00172)	0.127 (0.143)	0.00679 (0.00963)	0.00334 (0.00502)	0.0168 (0.022)	0.796 (0.802)	0.05 (0.0607)	0.0426 (0.0521)	0.059 (0.0709)
15q gain	88 (8%)	992	0.0142 (0.0189)	0.213 (0.232)	0.0128 (0.0173)	0.0222 (0.0284)	0.543 (0.557)	0.0984 (0.114)	0.0462 (0.0563)	0.0148 (0.0197)	0.0845 (0.0993)	0.0118 (0.016)	0.328 (0.349)	0.345 (0.366)
6p loss	190 (18%)	890	0.329 (0.35)	0.0477 (0.058)	1e-05 (2.35e-05)	0.115 (0.131)	0.962 (0.962)	0.00652 (0.00927)	0.00312 (0.00474)	0.00882 (0.0122)	0.0523 (0.0633)	0.00628 (0.00898)	0.455 (0.474)	0.646 (0.658)
11q loss	366 (34%)	714	0.091 (0.106)	0.102 (0.118)	1e-05 (2.35e-05)	1e-05 (2.35e-05)	0.413 (0.433)	0.151 (0.169)	1e-05 (2.35e-05)	0.00299 (0.00458)	0.0259 (0.0327)	0.00823 (0.0115)	0.632 (0.645)	0.125 (0.142)
21q loss	179 (17%)	901	0.039 (0.0481)	0.773 (0.779)	1e-05 (2.35e-05)	0.00072 (0.00123)	0.543 (0.557)	0.686 (0.694)	0.058 (0.0699)	0.00692 (0.00978)	0.0241 (0.0306)	0.00127 (0.00207)	0.222 (0.241)	0.0972 (0.113)
10p loss	175 (16%)	905	0.159 (0.178)	0.884 (0.885)	1e-05 (2.35e-05)	0.00062 (0.00107)	0.0868 (0.102)	0.186 (0.206)	0.00012 (0.000234)	1e-05 (2.35e-05)	0.00016 (0.000303)	0.0789 (0.093)	0.111 (0.127)	0.235 (0.255)
1q gain	708 (66%)	372	0.385 (0.405)	0.0965 (0.112)	1e-05 (2.35e-05)	0.19 (0.209)	0.627 (0.64)	0.111 (0.127)	1e-05 (2.35e-05)	0.00691 (0.00978)	0.0583 (0.0702)	0.00025 (0.000455)	0.25 (0.27)	0.302 (0.323)
17p gain	110 (10%)	970	0.169 (0.188)	0.681 (0.69)	1e-05 (2.35e-05)	0.0708 (0.0839)	0.845 (0.848)	0.486 (0.504)	0.0228 (0.029)	0.0589 (0.0708)	0.00488 (0.00709)	0.139 (0.156)	0.445 (0.464)	0.00172 (0.00276)
1q loss	48 (4%)	1032	0.00269 (0.00416)	0.203 (0.222)	7e-05 (0.000141)	0.475 (0.493)	0.285 (0.305)	0.516 (0.533)	0.00175 (0.0028)	0.105 (0.12)	0.0158 (0.0209)	0.138 (0.156)	0.183 (0.204)	0.422 (0.442)
16q gain	142 (13%)	938	0.0711 (0.0841)	0.74 (0.748)	0.00076 (0.00129)	0.0529 (0.064)	0.268 (0.288)	0.172 (0.192)	0.264 (0.284)	0.00303 (0.00462)	0.105 (0.12)	0.00081 (0.00136)	0.131 (0.148)	0.103 (0.119)
8q loss	93 (9%)	987	0.228 (0.248)	0.678 (0.689)	5e-05 (0.000103)	0.0917 (0.107)	0.396 (0.416)	0.52 (0.535)	0.00923 (0.0127)	0.0149 (0.0198)	0.374 (0.395)	0.447 (0.467)	0.361 (0.382)	0.802 (0.806)

'1p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
1P GAIN MUTATED	27	21	58
1P GAIN WILD-TYPE	202	95	110

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

'1p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
1P GAIN MUTATED	21	49	36
1P GAIN WILD-TYPE	138	217	52

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

'1p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
1P GAIN MUTATED	51	25	31	112	8
1P GAIN WILD-TYPE	279	107	264	182	21

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

'1p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
1P GAIN MUTATED	34	36	33	53	8
1P GAIN WILD-TYPE	184	147	112	86	80

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

'1p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
1P GAIN MUTATED	71	39	7	29	30	14	2
1P GAIN WILD-TYPE	123	198	23	175	101	53	8

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

'1p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
1P GAIN MUTATED	80	79	33
1P GAIN WILD-TYPE	140	319	222

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

'1p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S7. Gene #1: '1p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
1P GAIN MUTATED	39	43	20	32	84	5	3
1P GAIN WILD-TYPE	225	126	123	193	119	46	17

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

'1p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S8. Gene #1: '1p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
1P GAIN MUTATED	41	37	8	44	77	19
1P GAIN WILD-TYPE	248	126	82	246	106	41

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

'1p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
1P GAIN MUTATED	24	93	26	38	35	7
1P GAIN WILD-TYPE	115	177	182	178	147	39

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

'1p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
1P GAIN MUTATED	11	43	27	21	14	15	67	4	21
1P GAIN WILD-TYPE	55	80	157	165	60	98	92	69	62

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

'1p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
1P GAIN MUTATED	17	13	10	19	62	22
1P GAIN WILD-TYPE	116	79	49	100	83	92

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

'1p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.0018

Table S12. Gene #1: '1p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
1P GAIN MUTATED	87	39	17
1P GAIN WILD-TYPE	227	192	100

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

'1q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
1Q GAIN MUTATED	204	125	160	199	20
1Q GAIN WILD-TYPE	126	7	135	95	9

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

'1q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S14. Gene #2: '1q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
1Q GAIN MUTATED	135	118	85	187	134	36	11
1Q GAIN WILD-TYPE	129	51	58	38	69	15	9

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

'1q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00691 (Fisher's exact test), Q value = 0.0098

Table S15. Gene #2: '1q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
1Q GAIN MUTATED	169	123	56	200	121	37
1Q GAIN WILD-TYPE	120	40	34	90	62	23

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

'1q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
1Q GAIN MUTATED	35	87	125	99	58	85	106	48	53
1Q GAIN WILD-TYPE	31	36	59	87	16	28	53	25	30

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

'2p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S17. Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
2P GAIN MUTATED	6	6	48
2P GAIN WILD-TYPE	223	110	120

Figure S17. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
2P GAIN MUTATED	2	32	26
2P GAIN WILD-TYPE	157	234	62

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

'2p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
2P GAIN MUTATED	28	9	7	74	4
2P GAIN WILD-TYPE	302	123	288	220	25

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

'2p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S20. Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
2P GAIN MUTATED	4	20	13	44	2
2P GAIN WILD-TYPE	214	163	132	95	86

Figure S20. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S21. Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
2P GAIN MUTATED	49	4	2	11	20	14	2
2P GAIN WILD-TYPE	145	233	28	193	111	53	8

Figure S21. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S22. Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
2P GAIN MUTATED	64	22	16
2P GAIN WILD-TYPE	156	376	239

Figure S22. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S23. Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
2P GAIN MUTATED	11	42	1	3	64	0	1
2P GAIN WILD-TYPE	253	127	142	222	139	51	19

Figure S23. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S24. Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
2P GAIN MUTATED	8	27	1	5	58	23
2P GAIN WILD-TYPE	281	136	89	285	125	37

Figure S24. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S25. Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
2P GAIN MUTATED	14	79	3	7	11	3
2P GAIN WILD-TYPE	125	191	205	209	171	43

Figure S25. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S26. Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
2P GAIN MUTATED	7	23	4	3	4	3	47	1	25
2P GAIN WILD-TYPE	59	100	180	183	70	110	112	72	58

Figure S26. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S27. Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
2P GAIN MUTATED	11	5	3	3	47	10
2P GAIN WILD-TYPE	122	87	56	116	98	104

Figure S27. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S28. Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
2P GAIN MUTATED	58	16	5
2P GAIN WILD-TYPE	256	215	112

Figure S28. Get High-res Image Gene #3: '2p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'2q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S29. Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
2Q GAIN MUTATED	5	5	28
2Q GAIN WILD-TYPE	224	111	140

Figure S29. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'2q gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
2Q GAIN MUTATED	2	21	15
2Q GAIN WILD-TYPE	157	245	73

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

'2q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S31. Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
2Q GAIN MUTATED	16	8	7	41	1
2Q GAIN WILD-TYPE	314	124	288	253	28

Figure S31. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #3: 'CN_CNMF'

'2q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
2Q GAIN MUTATED	2	10	5	24	2
2Q GAIN WILD-TYPE	216	173	140	115	86

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

'2q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S33. Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
2Q GAIN MUTATED	29	2	3	5	12	7	2
2Q GAIN WILD-TYPE	165	235	27	199	119	60	8

Figure S33. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'2q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S34. Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
2Q GAIN MUTATED	40	10	10
2Q GAIN WILD-TYPE	180	388	245

Figure S34. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S35. Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
2Q GAIN MUTATED	4	27	1	4	37	0	0
2Q GAIN WILD-TYPE	260	142	142	221	166	51	20

Figure S35. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S36. Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
2Q GAIN MUTATED	4	21	1	3	33	11
2Q GAIN WILD-TYPE	285	142	89	287	150	49

Figure S36. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S37. Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
2Q GAIN MUTATED	6	44	3	5	8	3
2Q GAIN WILD-TYPE	133	226	205	211	174	43

Figure S37. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S38. Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
2Q GAIN MUTATED	3	15	4	1	3	3	22	0	18
2Q GAIN WILD-TYPE	63	108	180	185	71	110	137	73	65

Figure S38. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S39. Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
2Q GAIN MUTATED	6	4	3	2	30	6
2Q GAIN WILD-TYPE	127	88	56	117	115	108

Figure S39. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00835 (Fisher's exact test), Q value = 0.012

Table S40. Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
2Q GAIN MUTATED	35	11	5
2Q GAIN WILD-TYPE	279	220	112

Figure S40. Get High-res Image Gene #4: '2q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
3P GAIN MUTATED	56	23	3	49	6
3P GAIN WILD-TYPE	274	109	292	245	23

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

'3p gain' versus 'METHLYATION_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S42. Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
3P GAIN MUTATED	18	19	7	31	5
3P GAIN WILD-TYPE	200	164	138	108	83

Figure S42. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p gain' versus 'RPPA_CNMF'

P value = 0.0255 (Fisher's exact test), Q value = 0.032

Table S43. Gene #5: '3p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
3P GAIN MUTATED	34	31	5	14	12	11	1
3P GAIN WILD-TYPE	160	206	25	190	119	56	9

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

'3p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00774 (Fisher's exact test), Q value = 0.011

Table S44. Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
3P GAIN MUTATED	36	53	19
3P GAIN WILD-TYPE	184	345	236

Figure S44. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p gain' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S45. Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
3P GAIN MUTATED	36	20	6	27	42	1	5
3P GAIN WILD-TYPE	228	149	137	198	161	50	15

Figure S45. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S46. Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
3P GAIN MUTATED	47	24	2	18	40	6
3P GAIN WILD-TYPE	242	139	88	272	143	54

Figure S46. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p gain' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S47. Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
3P GAIN MUTATED	23	55	20	12	20	3
3P GAIN WILD-TYPE	116	215	188	204	162	43

Figure S47. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S48. Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
3P GAIN MUTATED	9	15	8	17	11	18	37	6	12
3P GAIN WILD-TYPE	57	108	176	169	63	95	122	67	71

Figure S48. Get High-res Image Gene #5: '3p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MRNA_CNMF'

P value = 0.00515 (Fisher's exact test), Q value = 0.0075

Table S49. Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
3Q GAIN MUTATED	47	16	50
3Q GAIN WILD-TYPE	182	100	118

Figure S49. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.016

Table S50. Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
3Q GAIN MUTATED	33	50	30
3Q GAIN WILD-TYPE	126	216	58

Figure S50. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
3Q GAIN MUTATED	72	29	10	95	7
3Q GAIN WILD-TYPE	258	103	285	199	22

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

'3q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S52. Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
3Q GAIN MUTATED	25	35	14	54	7
3Q GAIN WILD-TYPE	193	148	131	85	81

Figure S52. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q gain' versus 'RPPA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S53. Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
3Q GAIN MUTATED	62	38	5	24	28	15	1
3Q GAIN WILD-TYPE	132	199	25	180	103	52	9

Figure S53. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

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

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
3Q GAIN MUTATED	67	71	35
3Q GAIN WILD-TYPE	153	327	220

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

'3q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S55. Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
3Q GAIN MUTATED	48	36	9	31	81	2	6
3Q GAIN WILD-TYPE	216	133	134	194	122	49	14

Figure S55. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S56. Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
3Q GAIN MUTATED	54	37	3	30	75	14
3Q GAIN WILD-TYPE	235	126	87	260	108	46

Figure S56. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S57. Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
3Q GAIN MUTATED	28	99	27	20	30	5
3Q GAIN WILD-TYPE	111	171	181	196	152	41

Figure S57. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S58. Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
3Q GAIN MUTATED	11	24	9	31	12	22	63	12	25
3Q GAIN WILD-TYPE	55	99	175	155	62	91	96	61	58

Figure S58. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S59. Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
3Q GAIN MUTATED	17	11	8	17	55	15
3Q GAIN WILD-TYPE	116	81	51	102	90	99

Figure S59. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00087

Table S60. Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
3Q GAIN MUTATED	78	29	16
3Q GAIN WILD-TYPE	236	202	101

Figure S60. Get High-res Image Gene #6: '3q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.021

Table S61. Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
4P GAIN MUTATED	19	14	3
4P GAIN WILD-TYPE	140	252	85

Figure S61. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S62. Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
4P GAIN MUTATED	51	2	2	18	2
4P GAIN WILD-TYPE	279	130	293	276	27

Figure S62. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #3: 'CN_CNMF'

'4p gain' versus 'METHLYATION_CNMF'

P value = 0.00752 (Fisher's exact test), Q value = 0.011

Table S63. Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
4P GAIN MUTATED	10	24	7	8	3
4P GAIN WILD-TYPE	208	159	138	131	85

Figure S63. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p gain' versus 'RPPA_CNMF'

P value = 0.00162 (Fisher's exact test), Q value = 0.0026

Table S64. Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
4P GAIN MUTATED	9	23	7	7	14	6	0
4P GAIN WILD-TYPE	185	214	23	197	117	61	10

Figure S64. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p gain' versus 'MRNASEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S65. Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
4P GAIN MUTATED	38	11	7	9	9	1	0
4P GAIN WILD-TYPE	226	158	136	216	194	50	20

Figure S65. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.021

Table S66. Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
4P GAIN MUTATED	29	17	2	17	7	3
4P GAIN WILD-TYPE	260	146	88	273	176	57

Figure S66. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p gain' versus 'MIRSEQ_CNMF'

P value = 0.00696 (Fisher's exact test), Q value = 0.0098

Table S67. Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
4P GAIN MUTATED	19	17	16	7	10	5
4P GAIN WILD-TYPE	120	253	192	209	172	41

Figure S67. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.022

Table S68. Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
4P GAIN MUTATED	8	11	6	16	3	11	5	4	10
4P GAIN WILD-TYPE	58	112	178	170	71	102	154	69	73

Figure S68. Get High-res Image Gene #7: '4p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00491 (Fisher's exact test), Q value = 0.0071

Table S69. Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
4Q GAIN MUTATED	19	13	2
4Q GAIN WILD-TYPE	140	253	86

Figure S69. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S70. Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
4Q GAIN MUTATED	48	1	2	17	3
4Q GAIN WILD-TYPE	282	131	293	277	26

Figure S70. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #3: 'CN_CNMF'

'4q gain' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.021

Table S71. Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
4Q GAIN MUTATED	8	21	6	9	3
4Q GAIN WILD-TYPE	210	162	139	130	85

Figure S71. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q gain' versus 'RPPA_CNMF'

P value = 0.0212 (Fisher's exact test), Q value = 0.027

Table S72. Gene #8: '4q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
4Q GAIN MUTATED	7	22	6	11	13	4	0
4Q GAIN WILD-TYPE	187	215	24	193	118	63	10

Figure S72. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0284 (Fisher's exact test), Q value = 0.036

Table S73. Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
4Q GAIN MUTATED	8	37	18
4Q GAIN WILD-TYPE	212	361	237

Figure S73. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q gain' versus 'MRNASEQ_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S74. Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
4Q GAIN MUTATED	37	9	6	8	10	1	0
4Q GAIN WILD-TYPE	227	160	137	217	193	50	20

Figure S74. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q gain' versus 'MIRSEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.023

Table S75. Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
4Q GAIN MUTATED	18	18	14	7	9	4
4Q GAIN WILD-TYPE	121	252	194	209	173	42

Figure S75. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.052

Table S76. Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
4Q GAIN MUTATED	9	8	6	14	2	12	8	3	8
4Q GAIN WILD-TYPE	57	115	178	172	72	101	151	70	75

Figure S76. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0394 (Fisher's exact test), Q value = 0.048

Table S77. Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
4Q GAIN MUTATED	30	12	4
4Q GAIN WILD-TYPE	284	219	113

Figure S77. Get High-res Image Gene #8: '4q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.049

Table S78. Gene #9: '5p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
5P GAIN MUTATED	40	93	21
5P GAIN WILD-TYPE	119	173	67

Figure S78. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S79. Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
5P GAIN MUTATED	128	59	33	89	6
5P GAIN WILD-TYPE	202	73	262	205	23

Figure S79. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #3: 'CN_CNMF'

'5p gain' versus 'METHLYATION_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.015

Table S80. Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
5P GAIN MUTATED	63	66	29	44	19
5P GAIN WILD-TYPE	155	117	116	95	69

Figure S80. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p gain' versus 'MIRSEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.016

Table S81. Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
5P GAIN MUTATED	43	92	60	42	57	15
5P GAIN WILD-TYPE	96	178	148	174	125	31

Figure S81. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0138 (Fisher's exact test), Q value = 0.018

Table S82. Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
5P GAIN MUTATED	18	46	37	56	29	34	39	20	30
5P GAIN WILD-TYPE	48	77	147	130	45	79	120	53	53

Figure S82. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.022

Table S83. Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
5P GAIN MUTATED	39	31	25	35	40	20
5P GAIN WILD-TYPE	94	61	34	84	105	94

Figure S83. Get High-res Image Gene #9: '5p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q gain' versus 'MRNA_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.024

Table S84. Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
5Q GAIN MUTATED	53	28	22
5Q GAIN WILD-TYPE	176	88	146

Figure S84. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00353 (Fisher's exact test), Q value = 0.0053

Table S85. Gene #10: '5q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
5Q GAIN MUTATED	35	61	7
5Q GAIN WILD-TYPE	124	205	81

Figure S85. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S86. Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
5Q GAIN MUTATED	99	52	28	26	6
5Q GAIN WILD-TYPE	231	80	267	268	23

Figure S86. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #3: 'CN_CNMF'

'5q gain' versus 'METHLYATION_CNMF'

P value = 0.0018 (Fisher's exact test), Q value = 0.0029

Table S87. Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
5Q GAIN MUTATED	55	44	17	18	14
5Q GAIN WILD-TYPE	163	139	128	121	74

Figure S87. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q gain' versus 'RPPA_CNMF'

P value = 0.00302 (Fisher's exact test), Q value = 0.0046

Table S88. Gene #10: '5q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
5Q GAIN MUTATED	22	61	8	44	22	13	4
5Q GAIN WILD-TYPE	172	176	22	160	109	54	6

Figure S88. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.00044

Table S89. Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
5Q GAIN MUTATED	24	95	55
5Q GAIN WILD-TYPE	196	303	200

Figure S89. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q gain' versus 'MRNASEQ_CNMF'

P value = 0.00647 (Fisher's exact test), Q value = 0.0092

Table S90. Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
5Q GAIN MUTATED	54	33	28	60	23	7	4
5Q GAIN WILD-TYPE	210	136	115	165	180	44	16

Figure S90. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S91. Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
5Q GAIN MUTATED	72	38	16	59	16	8
5Q GAIN WILD-TYPE	217	125	74	231	167	52

Figure S91. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.021

Table S92. Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
5Q GAIN MUTATED	30	36	47	38	44	13
5Q GAIN WILD-TYPE	109	234	161	178	138	33

Figure S92. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S93. Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
5Q GAIN MUTATED	11	25	32	41	29	28	9	17	16
5Q GAIN WILD-TYPE	55	98	152	145	45	85	150	56	67

Figure S93. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S94. Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
5Q GAIN MUTATED	32	20	22	29	12	15
5Q GAIN WILD-TYPE	101	72	37	90	133	99

Figure S94. Get High-res Image Gene #10: '5q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S95. Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
6P GAIN MUTATED	32	9	56
6P GAIN WILD-TYPE	197	107	112

Figure S95. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6p gain' versus 'MRNA_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S96. Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
6P GAIN MUTATED	19	48	30
6P GAIN WILD-TYPE	140	218	58

Figure S96. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S97. Gene #11: '6p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
6P GAIN MUTATED	52	20	7	122	7
6P GAIN WILD-TYPE	278	112	288	172	22

Figure S97. 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 = 2.3e-05

Table S98. Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
6P GAIN MUTATED	23	41	16	64	2
6P GAIN WILD-TYPE	195	142	129	75	86

Figure S98. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S99. Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
6P GAIN MUTATED	59	26	7	21	29	18	3
6P GAIN WILD-TYPE	135	211	23	183	102	49	7

Figure S99. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S100. Gene #11: '6p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
6P GAIN MUTATED	67	62	34
6P GAIN WILD-TYPE	153	336	221

Figure S100. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S101. Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
6P GAIN MUTATED	38	39	7	21	89	4	9
6P GAIN WILD-TYPE	226	130	136	204	114	47	11

Figure S101. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S102. Gene #11: '6p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
6P GAIN MUTATED	36	50	2	27	80	12
6P GAIN WILD-TYPE	253	113	88	263	103	48

Figure S102. 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 = 2.3e-05

Table S103. Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
6P GAIN MUTATED	26	99	23	18	21	13
6P GAIN WILD-TYPE	113	171	185	198	161	33

Figure S103. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S104. Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
6P GAIN MUTATED	9	30	10	19	9	21	65	7	30
6P GAIN WILD-TYPE	57	93	174	167	65	92	94	66	53

Figure S104. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S105. Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
6P GAIN MUTATED	20	12	7	10	59	13
6P GAIN WILD-TYPE	113	80	52	109	86	101

Figure S105. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S106. Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
6P GAIN MUTATED	85	27	9
6P GAIN WILD-TYPE	229	204	108

Figure S106. Get High-res Image Gene #11: '6p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S107. Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
6Q GAIN MUTATED	17	8	45
6Q GAIN WILD-TYPE	212	108	123

Figure S107. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'6q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00119 (Fisher's exact test), Q value = 0.002

Table S108. Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
6Q GAIN MUTATED	14	33	23
6Q GAIN WILD-TYPE	145	233	65

Figure S108. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S109. Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
6Q GAIN MUTATED	29	14	3	100	3
6Q GAIN WILD-TYPE	301	118	292	194	26

Figure S109. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #3: 'CN_CNMF'

'6q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S110. Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
6Q GAIN MUTATED	13	27	15	45	2
6Q GAIN WILD-TYPE	205	156	130	94	86

Figure S110. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S111. Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
6Q GAIN MUTATED	44	18	4	11	25	16	2
6Q GAIN WILD-TYPE	150	219	26	193	106	51	8

Figure S111. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'6q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S112. Gene #12: '6q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
6Q GAIN MUTATED	54	45	21
6Q GAIN WILD-TYPE	166	353	234

Figure S112. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S113. Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
6Q GAIN MUTATED	23	26	4	17	66	4	8
6Q GAIN WILD-TYPE	241	143	139	208	137	47	12

Figure S113. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S114. Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
6Q GAIN MUTATED	24	36	2	20	58	8
6Q GAIN WILD-TYPE	265	127	88	270	125	52

Figure S114. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S115. Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
6Q GAIN MUTATED	19	76	15	13	13	7
6Q GAIN WILD-TYPE	120	194	193	203	169	39

Figure S115. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'6q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S116. Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
6Q GAIN MUTATED	5	23	7	12	5	16	44	6	25
6Q GAIN WILD-TYPE	61	100	177	174	69	97	115	67	58

Figure S116. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S117. Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
6Q GAIN MUTATED	13	10	4	9	47	11
6Q GAIN WILD-TYPE	120	82	55	110	98	103

Figure S117. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'6q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S118. Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
6Q GAIN MUTATED	67	21	6
6Q GAIN WILD-TYPE	247	210	111

Figure S118. Get High-res Image Gene #12: '6q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S119. Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
7P GAIN MUTATED	93	61	46	100	13
7P GAIN WILD-TYPE	237	71	249	194	16

Figure S119. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #3: 'CN_CNMF'

'7p gain' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 2e-04

Table S120. Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
7P GAIN MUTATED	59	63	24	56	22
7P GAIN WILD-TYPE	159	120	121	83	66

Figure S120. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S121. Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
7P GAIN MUTATED	70	70	26	61	73	11	1
7P GAIN WILD-TYPE	194	99	117	164	130	40	19

Figure S121. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S122. Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
7P GAIN MUTATED	76	63	20	61	65	27
7P GAIN WILD-TYPE	213	100	70	229	118	33

Figure S122. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p gain' versus 'MIRSEQ_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.0014

Table S123. Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
7P GAIN MUTATED	40	98	43	53	50	20
7P GAIN WILD-TYPE	99	172	165	163	132	26

Figure S123. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00284 (Fisher's exact test), Q value = 0.0044

Table S124. Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
7P GAIN MUTATED	18	50	40	38	26	34	54	20	24
7P GAIN WILD-TYPE	48	73	144	148	48	79	105	53	59

Figure S124. Get High-res Image Gene #13: '7p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.017

Table S125. Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
7Q GAIN MUTATED	48	23	55
7Q GAIN WILD-TYPE	181	93	113

Figure S125. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'7q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00869 (Fisher's exact test), Q value = 0.012

Table S126. Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
7Q GAIN MUTATED	32	61	33
7Q GAIN WILD-TYPE	127	205	55

Figure S126. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'7q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S127. Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
7Q GAIN MUTATED	72	53	38	94	11
7Q GAIN WILD-TYPE	258	79	257	200	18

Figure S127. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #3: 'CN_CNMF'

'7q gain' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

Table S128. Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
7Q GAIN MUTATED	50	44	21	53	19
7Q GAIN WILD-TYPE	168	139	124	86	69

Figure S128. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q gain' versus 'RPPA_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.055

Table S129. Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
7Q GAIN MUTATED	60	53	10	42	37	10	3
7Q GAIN WILD-TYPE	134	184	20	162	94	57	7

Figure S129. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0036

Table S130. Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
7Q GAIN MUTATED	73	92	50
7Q GAIN WILD-TYPE	147	306	205

Figure S130. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S131. Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
7Q GAIN MUTATED	56	55	22	50	77	7	0
7Q GAIN WILD-TYPE	208	114	121	175	126	44	20

Figure S131. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S132. Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
7Q GAIN MUTATED	61	48	16	48	72	22
7Q GAIN WILD-TYPE	228	115	74	242	111	38

Figure S132. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S133. Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
7Q GAIN MUTATED	26	97	33	47	40	18
7Q GAIN WILD-TYPE	113	173	175	169	142	28

Figure S133. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S134. Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
7Q GAIN MUTATED	12	40	37	28	22	25	62	16	19
7Q GAIN WILD-TYPE	54	83	147	158	52	88	97	57	64

Figure S134. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00293 (Fisher's exact test), Q value = 0.0045

Table S135. Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
7Q GAIN MUTATED	32	30	18	23	54	21
7Q GAIN WILD-TYPE	101	62	41	96	91	93

Figure S135. Get High-res Image Gene #14: '7q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.031 (Fisher's exact test), Q value = 0.038

Table S136. Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
8P GAIN MUTATED	53	59	27
8P GAIN WILD-TYPE	106	207	61

Figure S136. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S137. Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
8P GAIN MUTATED	94	41	45	90	21
8P GAIN WILD-TYPE	236	91	250	204	8

Figure S137. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #3: 'CN_CNMF'

'8p gain' versus 'METHLYATION_CNMF'

P value = 0.00095 (Fisher's exact test), Q value = 0.0016

Table S138. Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
8P GAIN MUTATED	53	49	25	55	23
8P GAIN WILD-TYPE	165	134	120	84	65

Figure S138. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p gain' versus 'MRNASEQ_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.00093

Table S139. Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
8P GAIN MUTATED	82	36	31	61	71	5	3
8P GAIN WILD-TYPE	182	133	112	164	132	46	17

Figure S139. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00138 (Fisher's exact test), Q value = 0.0022

Table S140. Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
8P GAIN MUTATED	90	42	16	64	66	11
8P GAIN WILD-TYPE	199	121	74	226	117	49

Figure S140. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.033

Table S141. Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
8P GAIN MUTATED	44	81	55	43	44	18
8P GAIN WILD-TYPE	95	189	153	173	138	28

Figure S141. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0386 (Fisher's exact test), Q value = 0.048

Table S142. Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
8P GAIN MUTATED	17	29	32	51	22	35	55	22	22
8P GAIN WILD-TYPE	49	94	152	135	52	78	104	51	61

Figure S142. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.024

Table S143. Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
8P GAIN MUTATED	36	16	15	23	52	29
8P GAIN WILD-TYPE	97	76	44	96	93	85

Figure S143. Get High-res Image Gene #15: '8p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MRNA_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.0081

Table S144. Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
8Q GAIN MUTATED	116	49	103
8Q GAIN WILD-TYPE	113	67	65

Figure S144. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'8q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.048

Table S145. Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
8Q GAIN MUTATED	84	128	56
8Q GAIN WILD-TYPE	75	138	32

Figure S145. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'8q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S146. Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
8Q GAIN MUTATED	191	51	71	189	28
8Q GAIN WILD-TYPE	139	81	224	105	1

Figure S146. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #3: 'CN_CNMF'

'8q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S147. Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
8Q GAIN MUTATED	86	96	57	96	28
8Q GAIN WILD-TYPE	132	87	88	43	60

Figure S147. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8q gain' versus 'RPPA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.014

Table S148. Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
8Q GAIN MUTATED	115	110	15	82	68	35	6
8Q GAIN WILD-TYPE	79	127	15	122	63	32	4

Figure S148. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'8q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0013

Table S149. Gene #16: '8q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
8Q GAIN MUTATED	126	202	103
8Q GAIN WILD-TYPE	94	196	152

Figure S149. 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 = 2.3e-05

Table S150. Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
8Q GAIN MUTATED	160	76	51	76	135	16	13
8Q GAIN WILD-TYPE	104	93	92	149	68	35	7

Figure S150. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S151. Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
8Q GAIN MUTATED	142	94	22	117	122	30
8Q GAIN WILD-TYPE	147	69	68	173	61	30

Figure S151. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S152. Gene #16: '8q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
8Q GAIN MUTATED	87	171	84	69	84	25
8Q GAIN WILD-TYPE	52	99	124	147	98	21

Figure S152. 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 = 2.3e-05

Table S153. Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
8Q GAIN MUTATED	36	69	47	77	37	66	105	36	47
8Q GAIN WILD-TYPE	30	54	137	109	37	47	54	37	36

Figure S153. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S154. Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
8Q GAIN MUTATED	65	30	21	51	106	42
8Q GAIN WILD-TYPE	68	62	38	68	39	72

Figure S154. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'8q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S155. Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
8Q GAIN MUTATED	186	85	44
8Q GAIN WILD-TYPE	128	146	73

Figure S155. Get High-res Image Gene #16: '8q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9p gain' versus 'MRNA_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.00041

Table S156. Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
9P GAIN MUTATED	16	16	36
9P GAIN WILD-TYPE	213	100	132

Figure S156. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S157. Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
9P GAIN MUTATED	12	25	31
9P GAIN WILD-TYPE	147	241	57

Figure S157. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S158. Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
9P GAIN MUTATED	17	36	15	66	5
9P GAIN WILD-TYPE	313	96	280	228	24

Figure S158. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #3: 'CN_CNMF'

'9p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S159. Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
9P GAIN MUTATED	25	16	14	38	3
9P GAIN WILD-TYPE	193	167	131	101	85

Figure S159. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p gain' versus 'RPPA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S160. Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
9P GAIN MUTATED	47	26	3	15	14	9	1
9P GAIN WILD-TYPE	147	211	27	189	117	58	9

Figure S160. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'9p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S161. Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
9P GAIN MUTATED	55	42	18
9P GAIN WILD-TYPE	165	356	237

Figure S161. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S162. Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
9P GAIN MUTATED	15	20	9	24	64	5	2
9P GAIN WILD-TYPE	249	149	134	201	139	46	18

Figure S162. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S163. Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
9P GAIN MUTATED	24	21	4	27	58	5
9P GAIN WILD-TYPE	265	142	86	263	125	55

Figure S163. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S164. Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
9P GAIN MUTATED	14	58	15	21	23	4
9P GAIN WILD-TYPE	125	212	193	195	159	42

Figure S164. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S165. Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
9P GAIN MUTATED	5	14	16	11	11	14	49	7	8
9P GAIN WILD-TYPE	61	109	168	175	63	99	110	66	75

Figure S165. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p gain' versus 'MIRSEQ_MATURE_CNMF'

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

Table S166. Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
9P GAIN MUTATED	15	8	9	19	32	5
9P GAIN WILD-TYPE	118	84	50	100	113	109

Figure S166. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.049 (Fisher's exact test), Q value = 0.059

Table S167. Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
9P GAIN MUTATED	47	21	20
9P GAIN WILD-TYPE	267	210	97

Figure S167. Get High-res Image Gene #17: '9p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S168. Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
9Q GAIN MUTATED	24	38	15	42	3
9Q GAIN WILD-TYPE	306	94	280	252	26

Figure S168. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #3: 'CN_CNMF'

'9q gain' versus 'METHLYATION_CNMF'

P value = 0.00104 (Fisher's exact test), Q value = 0.0017

Table S169. Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
9Q GAIN MUTATED	28	22	10	25	2
9Q GAIN WILD-TYPE	190	161	135	114	86

Figure S169. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00679 (Fisher's exact test), Q value = 0.0096

Table S170. Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
9Q GAIN MUTATED	37	45	19
9Q GAIN WILD-TYPE	183	353	236

Figure S170. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q gain' versus 'MRNASEQ_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.005

Table S171. Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
9Q GAIN MUTATED	19	24	10	25	38	4	2
9Q GAIN WILD-TYPE	245	145	133	200	165	47	18

Figure S171. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.022

Table S172. Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
9Q GAIN MUTATED	30	21	5	25	33	8
9Q GAIN WILD-TYPE	259	142	85	265	150	52

Figure S172. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.052

Table S173. Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
9Q GAIN MUTATED	16	8	9	19	24	6
9Q GAIN WILD-TYPE	117	84	50	100	121	108

Figure S173. Get High-res Image Gene #18: '9q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S174. Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
10P GAIN MUTATED	29	16	64
10P GAIN WILD-TYPE	200	100	104

Figure S174. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S175. Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
10P GAIN MUTATED	15	56	38
10P GAIN WILD-TYPE	144	210	50

Figure S175. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S176. Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
10P GAIN MUTATED	53	24	11	117	3
10P GAIN WILD-TYPE	277	108	284	177	26

Figure S176. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #3: 'CN_CNMF'

'10p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S177. Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
10P GAIN MUTATED	16	35	24	61	2
10P GAIN WILD-TYPE	202	148	121	78	86

Figure S177. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S178. Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
10P GAIN MUTATED	68	24	8	24	27	20	4
10P GAIN WILD-TYPE	126	213	22	180	104	47	6

Figure S178. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S179. Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
10P GAIN MUTATED	79	67	29
10P GAIN WILD-TYPE	141	331	226

Figure S179. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S180. Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
10P GAIN MUTATED	41	40	13	18	86	4	6
10P GAIN WILD-TYPE	223	129	130	207	117	47	14

Figure S180. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S181. Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
10P GAIN MUTATED	32	39	3	34	80	20
10P GAIN WILD-TYPE	257	124	87	256	103	40

Figure S181. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S182. Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
10P GAIN MUTATED	28	99	12	23	34	8
10P GAIN WILD-TYPE	111	171	196	193	148	38

Figure S182. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S183. Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
10P GAIN MUTATED	10	34	11	14	8	27	65	8	27
10P GAIN WILD-TYPE	56	89	173	172	66	86	94	65	56

Figure S183. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S184. Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
10P GAIN MUTATED	20	10	8	13	60	14
10P GAIN WILD-TYPE	113	82	51	106	85	100

Figure S184. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S185. Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
10P GAIN MUTATED	88	24	13
10P GAIN WILD-TYPE	226	207	104

Figure S185. Get High-res Image Gene #19: '10p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10q gain' versus 'MRNA_CNMF'

P value = 0.00307 (Fisher's exact test), Q value = 0.0047

Table S186. Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
10Q GAIN MUTATED	19	12	33
10Q GAIN WILD-TYPE	210	104	135

Figure S186. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.051

Table S187. Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
10Q GAIN MUTATED	13	34	17
10Q GAIN WILD-TYPE	146	232	71

Figure S187. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S188. Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
10Q GAIN MUTATED	33	20	8	52	1
10Q GAIN WILD-TYPE	297	112	287	242	28

Figure S188. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #3: 'CN_CNMF'

'10q gain' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.00094

Table S189. Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
10Q GAIN MUTATED	12	19	13	22	1
10Q GAIN WILD-TYPE	206	164	132	117	87

Figure S189. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q gain' versus 'RPPA_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.014

Table S190. Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
10Q GAIN MUTATED	33	19	5	17	10	12	1
10Q GAIN WILD-TYPE	161	218	25	187	121	55	9

Figure S190. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q gain' versus 'MRNASEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0012

Table S191. Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
10Q GAIN MUTATED	27	23	8	16	32	2	6
10Q GAIN WILD-TYPE	237	146	135	209	171	49	14

Figure S191. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S192. Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
10Q GAIN MUTATED	26	25	2	20	29	12
10Q GAIN WILD-TYPE	263	138	88	270	154	48

Figure S192. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_CNMF'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S193. Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
10Q GAIN MUTATED	19	43	9	15	19	7
10Q GAIN WILD-TYPE	120	227	199	201	163	39

Figure S193. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S194. Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
10Q GAIN MUTATED	7	18	9	7	7	19	27	4	14
10Q GAIN WILD-TYPE	59	105	175	179	67	94	132	69	69

Figure S194. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00266 (Fisher's exact test), Q value = 0.0041

Table S195. Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
10Q GAIN MUTATED	13	5	6	8	28	6
10Q GAIN WILD-TYPE	120	87	53	111	117	108

Figure S195. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.032

Table S196. Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
10Q GAIN MUTATED	41	14	11
10Q GAIN WILD-TYPE	273	217	106

Figure S196. Get High-res Image Gene #20: '10q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S197. Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
11P GAIN MUTATED	57	16	12	56	0
11P GAIN WILD-TYPE	273	116	283	238	29

Figure S197. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #3: 'CN_CNMF'

'11p gain' versus 'METHLYATION_CNMF'

P value = 0.00437 (Fisher's exact test), Q value = 0.0064

Table S198. Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
11P GAIN MUTATED	29	23	8	28	8
11P GAIN WILD-TYPE	189	160	137	111	80

Figure S198. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p gain' versus 'RPPA_CNMF'

P value = 0.0455 (Fisher's exact test), Q value = 0.055

Table S199. Gene #21: '11p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
11P GAIN MUTATED	39	23	3	25	14	11	0
11P GAIN WILD-TYPE	155	214	27	179	117	56	10

Figure S199. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p gain' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S200. Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
11P GAIN MUTATED	43	30	9	16	37	4	1
11P GAIN WILD-TYPE	221	139	134	209	166	47	19

Figure S200. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00843 (Fisher's exact test), Q value = 0.012

Table S201. Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
11P GAIN MUTATED	37	29	7	25	34	8
11P GAIN WILD-TYPE	252	134	83	265	149	52

Figure S201. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S202. Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
11P GAIN MUTATED	23	48	24	10	26	8
11P GAIN WILD-TYPE	116	222	184	206	156	38

Figure S202. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S203. Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
11P GAIN MUTATED	13	18	8	22	7	22	28	4	17
11P GAIN WILD-TYPE	53	105	176	164	67	91	131	69	66

Figure S203. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.0033

Table S204. Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
11P GAIN MUTATED	23	9	11	13	25	4
11P GAIN WILD-TYPE	110	83	48	106	120	110

Figure S204. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S205. Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
11P GAIN MUTATED	58	11	16
11P GAIN WILD-TYPE	256	220	101

Figure S205. Get High-res Image Gene #21: '11p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q gain' versus 'MRNA_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.043

Table S206. Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
11Q GAIN MUTATED	14	12	23
11Q GAIN WILD-TYPE	215	104	145

Figure S206. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'11q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S207. Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
11Q GAIN MUTATED	28	12	7	48	1
11Q GAIN WILD-TYPE	302	120	288	246	28

Figure S207. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #3: 'CN_CNMF'

'11q gain' versus 'METHLYATION_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.0018

Table S208. Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
11Q GAIN MUTATED	17	12	6	25	6
11Q GAIN WILD-TYPE	201	171	139	114	82

Figure S208. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11q gain' versus 'RPPA_CNMF'

P value = 0.00145 (Fisher's exact test), Q value = 0.0024

Table S209. Gene #22: '11q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
11Q GAIN MUTATED	29	10	3	16	9	11	0
11Q GAIN WILD-TYPE	165	227	27	188	122	56	10

Figure S209. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'11q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

Table S210. Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
11Q GAIN MUTATED	34	26	18
11Q GAIN WILD-TYPE	186	372	237

Figure S210. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11q gain' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.00069

Table S211. Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
11Q GAIN MUTATED	19	25	8	14	29	0	1
11Q GAIN WILD-TYPE	245	144	135	211	174	51	19

Figure S211. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 5e-04 (Fisher's exact test), Q value = 0.00088

Table S212. Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
11Q GAIN MUTATED	19	18	5	16	27	11
11Q GAIN WILD-TYPE	270	145	85	274	156	49

Figure S212. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S213. Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
11Q GAIN MUTATED	11	43	13	7	13	6
11Q GAIN WILD-TYPE	128	227	195	209	169	40

Figure S213. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00272 (Fisher's exact test), Q value = 0.0042

Table S214. Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
11Q GAIN MUTATED	7	11	4	16	5	10	22	5	13
11Q GAIN WILD-TYPE	59	112	180	170	69	103	137	68	70

Figure S214. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.037

Table S215. Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
11Q GAIN MUTATED	10	7	6	7	20	3
11Q GAIN WILD-TYPE	123	85	53	112	125	111

Figure S215. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.016

Table S216. Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
11Q GAIN MUTATED	33	9	11
11Q GAIN WILD-TYPE	281	222	106

Figure S216. Get High-res Image Gene #22: '11q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12p gain' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S217. Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
12P GAIN MUTATED	49	12	51
12P GAIN WILD-TYPE	180	104	117

Figure S217. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.032

Table S218. Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
12P GAIN MUTATED	33	50	29
12P GAIN WILD-TYPE	126	216	59

Figure S218. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S219. Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
12P GAIN MUTATED	98	27	9	88	3
12P GAIN WILD-TYPE	232	105	286	206	26

Figure S219. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #3: 'CN_CNMF'

'12p gain' versus 'METHLYATION_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S220. Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
12P GAIN MUTATED	44	40	17	44	8
12P GAIN WILD-TYPE	174	143	128	95	80

Figure S220. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p gain' versus 'RPPA_CNMF'

P value = 0.00332 (Fisher's exact test), Q value = 0.005

Table S221. Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
12P GAIN MUTATED	61	53	3	35	26	8	2
12P GAIN WILD-TYPE	133	184	27	169	105	59	8

Figure S221. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0116 (Fisher's exact test), Q value = 0.016

Table S222. Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
12P GAIN MUTATED	60	87	41
12P GAIN WILD-TYPE	160	311	214

Figure S222. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S223. Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
12P GAIN MUTATED	69	45	15	28	60	4	3
12P GAIN WILD-TYPE	195	124	128	197	143	47	17

Figure S223. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S224. Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
12P GAIN MUTATED	62	50	7	36	56	13
12P GAIN WILD-TYPE	227	113	83	254	127	47

Figure S224. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S225. Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
12P GAIN MUTATED	36	89	34	22	27	10
12P GAIN WILD-TYPE	103	181	174	194	155	36

Figure S225. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S226. Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
12P GAIN MUTATED	16	28	17	30	19	22	48	15	23
12P GAIN WILD-TYPE	50	95	167	156	55	91	111	58	60

Figure S226. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.0068

Table S227. Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
12P GAIN MUTATED	31	17	9	18	45	15
12P GAIN WILD-TYPE	102	75	50	101	100	99

Figure S227. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.0059

Table S228. Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
12P GAIN MUTATED	81	38	16
12P GAIN WILD-TYPE	233	193	101

Figure S228. Get High-res Image Gene #23: '12p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q gain' versus 'MRNA_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0011

Table S229. Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
12Q GAIN MUTATED	51	8	35
12Q GAIN WILD-TYPE	178	108	133

Figure S229. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S230. Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
12Q GAIN MUTATED	101	26	10	45	4
12Q GAIN WILD-TYPE	229	106	285	249	25

Figure S230. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #3: 'CN_CNMF'

'12q gain' versus 'METHLYATION_CNMF'

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

Table S231. Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
12Q GAIN MUTATED	46	39	13	20	8
12Q GAIN WILD-TYPE	172	144	132	119	80

Figure S231. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.033

Table S232. Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
12Q GAIN MUTATED	32	88	39
12Q GAIN WILD-TYPE	188	310	216

Figure S232. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S233. Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
12Q GAIN MUTATED	67	44	15	30	23	4	2
12Q GAIN WILD-TYPE	197	125	128	195	180	47	18

Figure S233. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S234. Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
12Q GAIN MUTATED	66	49	6	34	21	9
12Q GAIN WILD-TYPE	223	114	84	256	162	51

Figure S234. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q gain' versus 'MIRSEQ_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00091

Table S235. Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
12Q GAIN MUTATED	35	54	34	18	31	9
12Q GAIN WILD-TYPE	104	216	174	198	151	37

Figure S235. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0037

Table S236. Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
12Q GAIN MUTATED	16	28	17	33	18	19	17	16	17
12Q GAIN WILD-TYPE	50	95	167	153	56	94	142	57	66

Figure S236. Get High-res Image Gene #24: '12q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q gain' versus 'CN_CNMF'

P value = 0.00142 (Fisher's exact test), Q value = 0.0023

Table S237. Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
13Q GAIN MUTATED	31	7	14	40	1
13Q GAIN WILD-TYPE	299	125	281	254	28

Figure S237. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #3: 'CN_CNMF'

'13q gain' versus 'METHLYATION_CNMF'

P value = 0.00091 (Fisher's exact test), Q value = 0.0015

Table S238. Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
13Q GAIN MUTATED	9	19	9	20	2
13Q GAIN WILD-TYPE	209	164	136	119	86

Figure S238. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q gain' versus 'RPPA_CNMF'

P value = 0.00599 (Fisher's exact test), Q value = 0.0086

Table S239. Gene #25: '13q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
13Q GAIN MUTATED	24	20	1	7	16	10	1
13Q GAIN WILD-TYPE	170	217	29	197	115	57	9

Figure S239. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00246 (Fisher's exact test), Q value = 0.0038

Table S240. Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
13Q GAIN MUTATED	30	37	12
13Q GAIN WILD-TYPE	190	361	243

Figure S240. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q gain' versus 'MRNASEQ_CNMF'

P value = 0.00604 (Fisher's exact test), Q value = 0.0087

Table S241. Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
13Q GAIN MUTATED	22	19	6	16	29	1	0
13Q GAIN WILD-TYPE	242	150	137	209	174	50	20

Figure S241. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S242. Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
13Q GAIN MUTATED	26	17	3	12	24	11
13Q GAIN WILD-TYPE	263	146	87	278	159	49

Figure S242. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q gain' versus 'MIRSEQ_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.012

Table S243. Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
13Q GAIN MUTATED	13	37	14	9	14	4
13Q GAIN WILD-TYPE	126	233	194	207	168	42

Figure S243. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S244. Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
13Q GAIN MUTATED	9	11	5	7	9	9	18	8	15
13Q GAIN WILD-TYPE	57	112	179	179	65	104	141	65	68

Figure S244. Get High-res Image Gene #25: '13q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.019 (Fisher's exact test), Q value = 0.025

Table S245. Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
14Q GAIN MUTATED	24	46	5
14Q GAIN WILD-TYPE	135	220	83

Figure S245. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S246. Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
14Q GAIN MUTATED	69	25	20	26	3
14Q GAIN WILD-TYPE	261	107	275	268	26

Figure S246. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #3: 'CN_CNMF'

'14q gain' versus 'METHLYATION_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.00083

Table S247. Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
14Q GAIN MUTATED	27	38	8	12	8
14Q GAIN WILD-TYPE	191	145	137	127	80

Figure S247. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0233 (Fisher's exact test), Q value = 0.03

Table S248. Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
14Q GAIN MUTATED	27	65	23
14Q GAIN WILD-TYPE	193	333	232

Figure S248. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q gain' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S249. Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
14Q GAIN MUTATED	38	39	11	35	15	2	2
14Q GAIN WILD-TYPE	226	130	132	190	188	49	18

Figure S249. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S250. Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
14Q GAIN MUTATED	44	34	7	32	11	14
14Q GAIN WILD-TYPE	245	129	83	258	172	46

Figure S250. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q gain' versus 'MIRSEQ_CNMF'

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

Table S251. Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
14Q GAIN MUTATED	24	32	22	18	32	14
14Q GAIN WILD-TYPE	115	238	186	198	150	32

Figure S251. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S252. Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
14Q GAIN MUTATED	14	23	14	18	17	23	9	9	15
14Q GAIN WILD-TYPE	52	100	170	168	57	90	150	64	68

Figure S252. Get High-res Image Gene #26: '14q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q gain' versus 'MRNA_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.019

Table S253. Gene #27: '15q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
15Q GAIN MUTATED	16	6	24
15Q GAIN WILD-TYPE	213	110	144

Figure S253. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q gain' versus 'CN_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.017

Table S254. Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
15Q GAIN MUTATED	33	10	12	32	1
15Q GAIN WILD-TYPE	297	122	283	262	28

Figure S254. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #3: 'CN_CNMF'

'15q gain' versus 'METHLYATION_CNMF'

P value = 0.0222 (Fisher's exact test), Q value = 0.028

Table S255. Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
15Q GAIN MUTATED	10	14	6	17	10
15Q GAIN WILD-TYPE	208	169	139	122	78

Figure S255. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q gain' versus 'MRNASEQ_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.056

Table S256. Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
15Q GAIN MUTATED	23	16	8	12	26	1	2
15Q GAIN WILD-TYPE	241	153	135	213	177	50	18

Figure S256. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.02

Table S257. Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
15Q GAIN MUTATED	26	15	3	14	23	7
15Q GAIN WILD-TYPE	263	148	87	276	160	53

Figure S257. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.016

Table S258. Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
15Q GAIN MUTATED	6	14	4	12	7	10	16	6	12
15Q GAIN WILD-TYPE	60	109	180	174	67	103	143	67	71

Figure S258. Get High-res Image Gene #27: '15q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MRNA_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.005

Table S259. Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
16P GAIN MUTATED	126	43	73
16P GAIN WILD-TYPE	103	73	95

Figure S259. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'16p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0102 (Fisher's exact test), Q value = 0.014

Table S260. Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
16P GAIN MUTATED	83	130	29
16P GAIN WILD-TYPE	76	136	59

Figure S260. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S261. Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
16P GAIN MUTATED	150	86	104	108	14
16P GAIN WILD-TYPE	180	46	191	186	15

Figure S261. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #3: 'CN_CNMF'

'16p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S262. Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
16P GAIN MUTATED	113	85	38	42	28
16P GAIN WILD-TYPE	105	98	107	97	60

Figure S262. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p gain' versus 'RPPA_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.0069

Table S263. Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
16P GAIN MUTATED	60	118	13	85	58	34	5
16P GAIN WILD-TYPE	134	119	17	119	73	33	5

Figure S263. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00123 (Fisher's exact test), Q value = 0.002

Table S264. Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
16P GAIN MUTATED	71	184	118
16P GAIN WILD-TYPE	149	214	137

Figure S264. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S265. Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
16P GAIN MUTATED	103	80	58	135	53	22	10
16P GAIN WILD-TYPE	161	89	85	90	150	29	10

Figure S265. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S266. Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
16P GAIN MUTATED	142	80	34	133	47	25
16P GAIN WILD-TYPE	147	83	56	157	136	35

Figure S266. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_CNMF'

P value = 0.00051 (Fisher's exact test), Q value = 9e-04

Table S267. Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
16P GAIN MUTATED	59	94	92	83	94	29
16P GAIN WILD-TYPE	80	176	116	133	88	17

Figure S267. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S268. Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
16P GAIN MUTATED	25	56	75	78	43	64	36	32	42
16P GAIN WILD-TYPE	41	67	109	108	31	49	123	41	41

Figure S268. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S269. Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
16P GAIN MUTATED	62	42	27	64	38	42
16P GAIN WILD-TYPE	71	50	32	55	107	72

Figure S269. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00695 (Fisher's exact test), Q value = 0.0098

Table S270. Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
16P GAIN MUTATED	116	96	63
16P GAIN WILD-TYPE	198	135	54

Figure S270. Get High-res Image Gene #28: '16p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16q gain' versus 'CN_CNMF'

P value = 0.00076 (Fisher's exact test), Q value = 0.0013

Table S271. Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
16Q GAIN MUTATED	54	18	21	48	1
16Q GAIN WILD-TYPE	276	114	274	246	28

Figure S271. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #3: 'CN_CNMF'

'16q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00303 (Fisher's exact test), Q value = 0.0046

Table S272. Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
16Q GAIN MUTATED	41	26	4	29	26	15
16Q GAIN WILD-TYPE	248	137	86	261	157	45

Figure S272. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

Table S273. Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
16Q GAIN MUTATED	12	19	13	24	5	14	20	8	24
16Q GAIN WILD-TYPE	54	104	171	162	69	99	139	65	59

Figure S273. Get High-res Image Gene #29: '16q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S274. Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
17P GAIN MUTATED	55	11	10	30	4
17P GAIN WILD-TYPE	275	121	285	264	25

Figure S274. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #3: 'CN_CNMF'

'17p gain' versus 'MRNASEQ_CNMF'

P value = 0.0228 (Fisher's exact test), Q value = 0.029

Table S275. Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
17P GAIN MUTATED	38	17	10	12	24	5	3
17P GAIN WILD-TYPE	226	152	133	213	179	46	17

Figure S275. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p gain' versus 'MIRSEQ_CNMF'

P value = 0.00488 (Fisher's exact test), Q value = 0.0071

Table S276. Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
17P GAIN MUTATED	27	29	20	16	11	4
17P GAIN WILD-TYPE	112	241	188	200	171	42

Figure S276. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00172 (Fisher's exact test), Q value = 0.0028

Table S277. Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
17P GAIN MUTATED	47	17	6
17P GAIN WILD-TYPE	267	214	111

Figure S277. Get High-res Image Gene #30: '17p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.015

Table S278. Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
17Q GAIN MUTATED	38	53	8
17Q GAIN WILD-TYPE	121	213	80

Figure S278. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S279. Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
17Q GAIN MUTATED	138	14	18	41	10
17Q GAIN WILD-TYPE	192	118	277	253	19

Figure S279. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #3: 'CN_CNMF'

'17q gain' versus 'METHLYATION_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.00075

Table S280. Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
17Q GAIN MUTATED	46	58	22	19	15
17Q GAIN WILD-TYPE	172	125	123	120	73

Figure S280. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q gain' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S281. Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
17Q GAIN MUTATED	26	108	51
17Q GAIN WILD-TYPE	194	290	204

Figure S281. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S282. Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
17Q GAIN MUTATED	101	35	20	25	26	7	6
17Q GAIN WILD-TYPE	163	134	123	200	177	44	14

Figure S282. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S283. Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
17Q GAIN MUTATED	91	40	6	54	21	8
17Q GAIN WILD-TYPE	198	123	84	236	162	52

Figure S283. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S284. Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
17Q GAIN MUTATED	53	46	48	29	33	7
17Q GAIN WILD-TYPE	86	224	160	187	149	39

Figure S284. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S285. Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
17Q GAIN MUTATED	27	21	22	50	9	27	17	22	21
17Q GAIN WILD-TYPE	39	102	162	136	65	86	142	51	62

Figure S285. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00154 (Fisher's exact test), Q value = 0.0025

Table S286. Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
17Q GAIN MUTATED	36	9	12	37	25	20
17Q GAIN WILD-TYPE	97	83	47	82	120	94

Figure S286. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00649 (Fisher's exact test), Q value = 0.0092

Table S287. Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
17Q GAIN MUTATED	82	35	22
17Q GAIN WILD-TYPE	232	196	95

Figure S287. Get High-res Image Gene #31: '17q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p gain' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S288. Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
18P GAIN MUTATED	34	9	44
18P GAIN WILD-TYPE	195	107	124

Figure S288. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p gain' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S289. Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
18P GAIN MUTATED	26	29	32
18P GAIN WILD-TYPE	133	237	56

Figure S289. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S290. Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
18P GAIN MUTATED	50	24	10	83	10
18P GAIN WILD-TYPE	280	108	285	211	19

Figure S290. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #3: 'CN_CNMF'

'18p gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S291. Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
18P GAIN MUTATED	28	16	12	53	4
18P GAIN WILD-TYPE	190	167	133	86	84

Figure S291. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p gain' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S292. Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
18P GAIN MUTATED	58	29	3	19	18	15	1
18P GAIN WILD-TYPE	136	208	27	185	113	52	9

Figure S292. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S293. Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
18P GAIN MUTATED	61	59	23
18P GAIN WILD-TYPE	159	339	232

Figure S293. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S294. Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
18P GAIN MUTATED	39	22	5	35	73	0	3
18P GAIN WILD-TYPE	225	147	138	190	130	51	17

Figure S294. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S295. Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
18P GAIN MUTATED	50	21	3	20	69	14
18P GAIN WILD-TYPE	239	142	87	270	114	46

Figure S295. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S296. Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
18P GAIN MUTATED	22	82	22	11	27	6
18P GAIN WILD-TYPE	117	188	186	205	155	40

Figure S296. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S297. Gene #32: '18p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
18P GAIN MUTATED	12	20	10	18	11	12	59	9	19
18P GAIN WILD-TYPE	54	103	174	168	63	101	100	64	64

Figure S297. 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 = 2.3e-05

Table S298. Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
18P GAIN MUTATED	19	5	7	14	56	8
18P GAIN WILD-TYPE	114	87	52	105	89	106

Figure S298. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S299. Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
18P GAIN MUTATED	74	20	15
18P GAIN WILD-TYPE	240	211	102

Figure S299. Get High-res Image Gene #32: '18p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18q gain' versus 'MRNA_CNMF'

P value = 0.00285 (Fisher's exact test), Q value = 0.0044

Table S300. Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
18Q GAIN MUTATED	37	8	36
18Q GAIN WILD-TYPE	192	108	132

Figure S300. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q gain' versus 'MRNA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S301. Gene #33: '18q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
18Q GAIN MUTATED	28	26	27
18Q GAIN WILD-TYPE	131	240	61

Figure S301. 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 = 2.3e-05

Table S302. Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
18Q GAIN MUTATED	47	24	7	67	9
18Q GAIN WILD-TYPE	283	108	288	227	20

Figure S302. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #3: 'CN_CNMF'

'18q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S303. Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
18Q GAIN MUTATED	29	16	10	37	4
18Q GAIN WILD-TYPE	189	167	135	102	84

Figure S303. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q gain' versus 'RPPA_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.0031

Table S304. Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
18Q GAIN MUTATED	46	29	2	19	18	11	0
18Q GAIN WILD-TYPE	148	208	28	185	113	56	10

Figure S304. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00633 (Fisher's exact test), Q value = 0.009

Table S305. Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
18Q GAIN MUTATED	43	58	24
18Q GAIN WILD-TYPE	177	340	231

Figure S305. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S306. Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
18Q GAIN MUTATED	41	11	5	36	57	1	3
18Q GAIN WILD-TYPE	223	158	138	189	146	50	17

Figure S306. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S307. Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
18Q GAIN MUTATED	51	17	3	24	53	6
18Q GAIN WILD-TYPE	238	146	87	266	130	54

Figure S307. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S308. Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
18Q GAIN MUTATED	26	60	21	11	25	5
18Q GAIN WILD-TYPE	113	210	187	205	157	41

Figure S308. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S309. Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
18Q GAIN MUTATED	14	14	10	20	11	12	45	9	13
18Q GAIN WILD-TYPE	52	109	174	166	63	101	114	64	70

Figure S309. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S310. Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
18Q GAIN MUTATED	19	5	5	12	36	9
18Q GAIN WILD-TYPE	114	87	54	107	109	105

Figure S310. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'18q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00483 (Fisher's exact test), Q value = 0.007

Table S311. Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
18Q GAIN MUTATED	54	18	14
18Q GAIN WILD-TYPE	260	213	103

Figure S311. Get High-res Image Gene #33: '18q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19p gain' versus 'MRNA_CNMF'

P value = 0.00069 (Fisher's exact test), Q value = 0.0012

Table S312. Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
19P GAIN MUTATED	27	19	45
19P GAIN WILD-TYPE	202	97	123

Figure S312. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0033 (Fisher's exact test), Q value = 0.005

Table S313. Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
19P GAIN MUTATED	19	46	26
19P GAIN WILD-TYPE	140	220	62

Figure S313. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S314. Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
19P GAIN MUTATED	45	35	19	82	6
19P GAIN WILD-TYPE	285	97	276	212	23

Figure S314. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #3: 'CN_CNMF'

'19p gain' versus 'METHLYATION_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.00045

Table S315. Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
19P GAIN MUTATED	24	31	19	41	12
19P GAIN WILD-TYPE	194	152	126	98	76

Figure S315. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p gain' versus 'RPPA_CNMF'

P value = 0.00237 (Fisher's exact test), Q value = 0.0037

Table S316. Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
19P GAIN MUTATED	52	32	4	26	31	11	1
19P GAIN WILD-TYPE	142	205	26	178	100	56	9

Figure S316. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00418 (Fisher's exact test), Q value = 0.0062

Table S317. Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
19P GAIN MUTATED	56	59	42
19P GAIN WILD-TYPE	164	339	213

Figure S317. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S318. Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
19P GAIN MUTATED	32	29	19	28	64	5	8
19P GAIN WILD-TYPE	232	140	124	197	139	46	12

Figure S318. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S319. Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
19P GAIN MUTATED	39	24	10	40	56	16
19P GAIN WILD-TYPE	250	139	80	250	127	44

Figure S319. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.00047

Table S320. Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
19P GAIN MUTATED	25	72	31	25	23	8
19P GAIN WILD-TYPE	114	198	177	191	159	38

Figure S320. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S321. Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
19P GAIN MUTATED	5	30	23	19	11	19	45	13	19
19P GAIN WILD-TYPE	61	93	161	167	63	94	114	60	64

Figure S321. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S322. Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
19P GAIN MUTATED	13	13	17	12	43	15
19P GAIN WILD-TYPE	120	79	42	107	102	99

Figure S322. Get High-res Image Gene #34: '19p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19q gain' versus 'MRNA_CNMF'

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

Table S323. Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
19Q GAIN MUTATED	36	24	51
19Q GAIN WILD-TYPE	193	92	117

Figure S323. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00745 (Fisher's exact test), Q value = 0.01

Table S324. Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
19Q GAIN MUTATED	27	54	30
19Q GAIN WILD-TYPE	132	212	58

Figure S324. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'19q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S325. Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
19Q GAIN MUTATED	60	39	22	90	8
19Q GAIN WILD-TYPE	270	93	273	204	21

Figure S325. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #3: 'CN_CNMF'

'19q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S326. Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
19Q GAIN MUTATED	28	37	19	46	14
19Q GAIN WILD-TYPE	190	146	126	93	74

Figure S326. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q gain' versus 'RPPA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.021

Table S327. Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
19Q GAIN MUTATED	57	39	6	35	30	13	0
19Q GAIN WILD-TYPE	137	198	24	169	101	54	10

Figure S327. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.0164 (Fisher's exact test), Q value = 0.021

Table S328. Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
19Q GAIN MUTATED	60	70	50
19Q GAIN WILD-TYPE	160	328	205

Figure S328. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S329. Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
19Q GAIN MUTATED	46	37	23	28	69	6	8
19Q GAIN WILD-TYPE	218	132	120	197	134	45	12

Figure S329. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S330. Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
19Q GAIN MUTATED	48	33	13	44	62	17
19Q GAIN WILD-TYPE	241	130	77	246	121	43

Figure S330. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S331. Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
19Q GAIN MUTATED	31	82	35	30	30	9
19Q GAIN WILD-TYPE	108	188	173	186	152	37

Figure S331. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S332. Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
19Q GAIN MUTATED	7	37	27	24	10	24	50	14	24
19Q GAIN WILD-TYPE	59	86	157	162	64	89	109	59	59

Figure S332. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00045 (Fisher's exact test), Q value = 8e-04

Table S333. Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
19Q GAIN MUTATED	24	14	17	15	47	17
19Q GAIN WILD-TYPE	109	78	42	104	98	97

Figure S333. Get High-res Image Gene #35: '19q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MRNA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S334. Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
20P GAIN MUTATED	87	34	89
20P GAIN WILD-TYPE	142	82	79

Figure S334. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S335. Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
20P GAIN MUTATED	172	62	24	141	12
20P GAIN WILD-TYPE	158	70	271	153	17

Figure S335. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #3: 'CN_CNMF'

'20p gain' versus 'METHLYATION_CNMF'

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

Table S336. Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
20P GAIN MUTATED	81	83	43	55	20
20P GAIN WILD-TYPE	137	100	102	84	68

Figure S336. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p gain' versus 'RPPA_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.018

Table S337. Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
20P GAIN MUTATED	85	85	17	62	46	32	4
20P GAIN WILD-TYPE	109	152	13	142	85	35	6

Figure S337. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00463 (Fisher's exact test), Q value = 0.0068

Table S338. Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
20P GAIN MUTATED	87	168	76
20P GAIN WILD-TYPE	133	230	179

Figure S338. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S339. Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
20P GAIN MUTATED	113	85	34	70	86	11	10
20P GAIN WILD-TYPE	151	84	109	155	117	40	10

Figure S339. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S340. Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
20P GAIN MUTATED	112	86	7	104	76	24
20P GAIN WILD-TYPE	177	77	83	186	107	36

Figure S340. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S341. Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
20P GAIN MUTATED	66	128	63	47	74	27
20P GAIN WILD-TYPE	73	142	145	169	108	19

Figure S341. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S342. Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
20P GAIN MUTATED	24	60	44	58	46	47	60	21	45
20P GAIN WILD-TYPE	42	63	140	128	28	66	99	52	38

Figure S342. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00858 (Fisher's exact test), Q value = 0.012

Table S343. Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
20P GAIN MUTATED	52	29	26	46	72	32
20P GAIN WILD-TYPE	81	63	33	73	73	82

Figure S343. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00312 (Fisher's exact test), Q value = 0.0047

Table S344. Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
20P GAIN MUTATED	140	70	47
20P GAIN WILD-TYPE	174	161	70

Figure S344. Get High-res Image Gene #36: '20p gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q gain' versus 'MRNA_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S345. Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
20Q GAIN MUTATED	97	35	94
20Q GAIN WILD-TYPE	132	81	74

Figure S345. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'20q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S346. Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
20Q GAIN MUTATED	202	61	26	149	12
20Q GAIN WILD-TYPE	128	71	269	145	17

Figure S346. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #3: 'CN_CNMF'

'20q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S347. Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
20Q GAIN MUTATED	89	100	42	62	19
20Q GAIN WILD-TYPE	129	83	103	77	69

Figure S347. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S348. Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
20Q GAIN MUTATED	144	87	35	69	88	13	12
20Q GAIN WILD-TYPE	120	82	108	156	115	38	8

Figure S348. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S349. Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
20Q GAIN MUTATED	132	94	7	111	76	28
20Q GAIN WILD-TYPE	157	69	83	179	107	32

Figure S349. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S350. Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
20Q GAIN MUTATED	79	134	78	48	77	28
20Q GAIN WILD-TYPE	60	136	130	168	105	18

Figure S350. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S351. Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
20Q GAIN MUTATED	31	66	45	68	44	59	61	23	47
20Q GAIN WILD-TYPE	35	57	139	118	30	54	98	50	36

Figure S351. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0011

Table S352. Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
20Q GAIN MUTATED	66	31	29	52	76	32
20Q GAIN WILD-TYPE	67	61	30	67	69	82

Figure S352. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S353. Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
20Q GAIN MUTATED	163	74	49
20Q GAIN WILD-TYPE	151	157	68

Figure S353. Get High-res Image Gene #37: '20q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S354. Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
21Q GAIN MUTATED	31	17	57
21Q GAIN WILD-TYPE	198	99	111

Figure S354. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00054 (Fisher's exact test), Q value = 0.00094

Table S355. Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
21Q GAIN MUTATED	18	60	27
21Q GAIN WILD-TYPE	141	206	61

Figure S355. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'21q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S356. Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
21Q GAIN MUTATED	49	25	17	100	7
21Q GAIN WILD-TYPE	281	107	278	194	22

Figure S356. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #3: 'CN_CNMF'

'21q gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S357. Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
21Q GAIN MUTATED	16	37	17	51	8
21Q GAIN WILD-TYPE	202	146	128	88	80

Figure S357. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q gain' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S358. Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
21Q GAIN MUTATED	55	29	5	23	32	14	4
21Q GAIN WILD-TYPE	139	208	25	181	99	53	6

Figure S358. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'21q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S359. Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
21Q GAIN MUTATED	72	56	34
21Q GAIN WILD-TYPE	148	342	221

Figure S359. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'21q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S360. Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
21Q GAIN MUTATED	34	49	10	23	72	4	5
21Q GAIN WILD-TYPE	230	120	133	202	131	47	15

Figure S360. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'21q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S361. Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
21Q GAIN MUTATED	38	43	4	25	62	25
21Q GAIN WILD-TYPE	251	120	86	265	121	35

Figure S361. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S362. Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
21Q GAIN MUTATED	28	84	18	26	27	10
21Q GAIN WILD-TYPE	111	186	190	190	155	36

Figure S362. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S363. Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
21Q GAIN MUTATED	7	36	12	19	12	19	53	10	25
21Q GAIN WILD-TYPE	59	87	172	167	62	94	106	63	58

Figure S363. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'21q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S364. Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
21Q GAIN MUTATED	18	8	9	16	52	15
21Q GAIN WILD-TYPE	115	84	50	103	93	99

Figure S364. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'21q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S365. Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
21Q GAIN MUTATED	81	28	9
21Q GAIN WILD-TYPE	233	203	108

Figure S365. Get High-res Image Gene #38: '21q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'22q gain' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S366. Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
22Q GAIN MUTATED	12	5	35
22Q GAIN WILD-TYPE	217	111	133

Figure S366. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.0079 (Fisher's exact test), Q value = 0.011

Table S367. Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
22Q GAIN MUTATED	8	29	15
22Q GAIN WILD-TYPE	151	237	73

Figure S367. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'22q gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S368. Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
22Q GAIN MUTATED	32	2	4	59	2
22Q GAIN WILD-TYPE	298	130	291	235	27

Figure S368. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #3: 'CN_CNMF'

'22q gain' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S369. Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
22Q GAIN MUTATED	11	22	10	21	0
22Q GAIN WILD-TYPE	207	161	135	118	88

Figure S369. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'22q gain' versus 'RPPA_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S370. Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
22Q GAIN MUTATED	30	10	4	10	17	12	1
22Q GAIN WILD-TYPE	164	227	26	194	114	55	9

Figure S370. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'22q gain' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S371. Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
22Q GAIN MUTATED	42	30	12
22Q GAIN WILD-TYPE	178	368	243

Figure S371. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S372. Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
22Q GAIN MUTATED	23	29	1	5	37	0	2
22Q GAIN WILD-TYPE	241	140	142	220	166	51	18

Figure S372. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S373. Gene #39: '22q gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
22Q GAIN MUTATED	21	23	0	8	32	13
22Q GAIN WILD-TYPE	268	140	90	282	151	47

Figure S373. 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 = 2.3e-05

Table S374. Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
22Q GAIN MUTATED	11	48	13	5	15	4
22Q GAIN WILD-TYPE	128	222	195	211	167	42

Figure S374. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S375. Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
22Q GAIN MUTATED	5	17	3	10	0	10	28	7	16
22Q GAIN WILD-TYPE	61	106	181	176	74	103	131	66	67

Figure S375. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S376. Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
22Q GAIN MUTATED	10	3	6	5	27	4
22Q GAIN WILD-TYPE	123	89	53	114	118	110

Figure S376. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'22q gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00391 (Fisher's exact test), Q value = 0.0058

Table S377. Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
22Q GAIN MUTATED	38	12	5
22Q GAIN WILD-TYPE	276	219	112

Figure S377. Get High-res Image Gene #39: '22q gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xp gain' versus 'MRNA_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.025

Table S378. Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
XP GAIN MUTATED	35	12	38
XP GAIN WILD-TYPE	194	104	130

Figure S378. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S379. Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
XP GAIN MUTATED	43	22	14	66	5
XP GAIN WILD-TYPE	287	110	281	228	24

Figure S379. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #3: 'CN_CNMF'

'xp gain' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S380. Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
XP GAIN MUTATED	24	28	6	34	6
XP GAIN WILD-TYPE	194	155	139	105	82

Figure S380. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp gain' versus 'RPPA_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.012

Table S381. Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
XP GAIN MUTATED	35	32	0	18	23	13	1
XP GAIN WILD-TYPE	159	205	30	186	108	54	9

Figure S381. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00833 (Fisher's exact test), Q value = 0.012

Table S382. Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
XP GAIN MUTATED	44	52	26
XP GAIN WILD-TYPE	176	346	229

Figure S382. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S383. Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
XP GAIN MUTATED	36	28	7	24	45	3	6
XP GAIN WILD-TYPE	228	141	136	201	158	48	14

Figure S383. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S384. Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
XP GAIN MUTATED	38	37	1	27	39	7
XP GAIN WILD-TYPE	251	126	89	263	144	53

Figure S384. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S385. Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
XP GAIN MUTATED	24	58	18	9	23	11
XP GAIN WILD-TYPE	115	212	190	207	159	35

Figure S385. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00012

Table S386. Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
XP GAIN MUTATED	7	22	9	20	15	16	32	5	17
XP GAIN WILD-TYPE	59	101	175	166	59	97	127	68	66

Figure S386. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S387. Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
XP GAIN MUTATED	17	8	5	12	35	4
XP GAIN WILD-TYPE	116	84	54	107	110	110

Figure S387. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S388. Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
XP GAIN MUTATED	56	15	10
XP GAIN WILD-TYPE	258	216	107

Figure S388. Get High-res Image Gene #40: 'xp gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq gain' versus 'MRNA_CNMF'

P value = 0.00453 (Fisher's exact test), Q value = 0.0066

Table S389. Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
XQ GAIN MUTATED	32	10	38
XQ GAIN WILD-TYPE	197	106	130

Figure S389. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq gain' versus 'MRNA_CHIERARCHICAL'

P value = 0.00677 (Fisher's exact test), Q value = 0.0096

Table S390. Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
XQ GAIN MUTATED	21	35	24
XQ GAIN WILD-TYPE	138	231	64

Figure S390. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xq gain' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S391. Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
XQ GAIN MUTATED	39	20	12	62	4
XQ GAIN WILD-TYPE	291	112	283	232	25

Figure S391. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #3: 'CN_CNMF'

'xq gain' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S392. Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
XQ GAIN MUTATED	23	20	4	33	5
XQ GAIN WILD-TYPE	195	163	141	106	83

Figure S392. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq gain' versus 'RPPA_CNMF'

P value = 0.0173 (Fisher's exact test), Q value = 0.023

Table S393. Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
XQ GAIN MUTATED	37	28	0	19	18	9	2
XQ GAIN WILD-TYPE	157	209	30	185	113	58	8

Figure S393. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq gain' versus 'RPPA_CHIERARCHICAL'

P value = 0.00049 (Fisher's exact test), Q value = 0.00087

Table S394. Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
XQ GAIN MUTATED	46	43	24
XQ GAIN WILD-TYPE	174	355	231

Figure S394. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq gain' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S395. Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
XQ GAIN MUTATED	32	22	5	20	50	3	4
XQ GAIN WILD-TYPE	232	147	138	205	153	48	16

Figure S395. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq gain' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S396. Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
XQ GAIN MUTATED	37	25	0	23	45	6
XQ GAIN WILD-TYPE	252	138	90	267	138	54

Figure S396. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S397. Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
XQ GAIN MUTATED	20	61	18	7	16	8
XQ GAIN WILD-TYPE	119	209	190	209	166	38

Figure S397. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq gain' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S398. Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
XQ GAIN MUTATED	3	17	11	22	13	12	36	4	12
XQ GAIN WILD-TYPE	63	106	173	164	61	101	123	69	71

Figure S398. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq gain' versus 'MIRSEQ_MATURE_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S399. Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
XQ GAIN MUTATED	13	7	6	8	33	4
XQ GAIN WILD-TYPE	120	85	53	111	112	110

Figure S399. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq gain' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00423 (Fisher's exact test), Q value = 0.0062

Table S400. Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
XQ GAIN MUTATED	47	16	8
XQ GAIN WILD-TYPE	267	215	109

Figure S400. Get High-res Image Gene #41: 'xq gain' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'1p loss' versus 'MRNA_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.029

Table S401. Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
1P LOSS MUTATED	64	19	32
1P LOSS WILD-TYPE	165	97	136

Figure S401. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.003

Table S402. Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
1P LOSS MUTATED	39	68	8
1P LOSS WILD-TYPE	120	198	80

Figure S402. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'1p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S403. Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
1P LOSS MUTATED	108	46	16	52	5
1P LOSS WILD-TYPE	222	86	279	242	24

Figure S403. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #3: 'CN_CNMF'

'1p loss' versus 'METHLYATION_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.00088

Table S404. Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
1P LOSS MUTATED	41	57	22	21	12
1P LOSS WILD-TYPE	177	126	123	118	76

Figure S404. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'1p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.021

Table S405. Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
1P LOSS MUTATED	34	97	45
1P LOSS WILD-TYPE	186	301	210

Figure S405. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'1p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S406. Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
1P LOSS MUTATED	74	56	13	47	22	8	5
1P LOSS WILD-TYPE	190	113	130	178	181	43	15

Figure S406. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S407. Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
1P LOSS MUTATED	79	60	7	51	20	8
1P LOSS WILD-TYPE	210	103	83	239	163	52

Figure S407. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.005

Table S408. Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
1P LOSS MUTATED	34	55	49	26	42	15
1P LOSS WILD-TYPE	105	215	159	190	140	31

Figure S408. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'1p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S409. Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
1P LOSS MUTATED	20	29	21	38	27	32	17	18	19
1P LOSS WILD-TYPE	46	94	163	148	47	81	142	55	64

Figure S409. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'1p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.022

Table S410. Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
1P LOSS MUTATED	33	16	6	22	14	21
1P LOSS WILD-TYPE	100	76	53	97	131	93

Figure S410. Get High-res Image Gene #42: '1p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'1q loss' versus 'MRNA_CNMF'

P value = 0.00269 (Fisher's exact test), Q value = 0.0042

Table S411. Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
1Q LOSS MUTATED	17	0	11
1Q LOSS WILD-TYPE	212	116	157

Figure S411. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'1q loss' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S412. Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
1Q LOSS MUTATED	26	3	2	15	2
1Q LOSS WILD-TYPE	304	129	293	279	27

Figure S412. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #3: 'CN_CNMF'

'1q loss' versus 'MRNASEQ_CNMF'

P value = 0.00175 (Fisher's exact test), Q value = 0.0028

Table S413. Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
1Q LOSS MUTATED	22	11	2	4	7	0	1
1Q LOSS WILD-TYPE	242	158	141	221	196	51	19

Figure S413. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'1q loss' versus 'MIRSEQ_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.021

Table S414. Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
1Q LOSS MUTATED	12	16	8	3	5	2
1Q LOSS WILD-TYPE	127	254	200	213	177	44

Figure S414. Get High-res Image Gene #43: '1q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MRNA_CNMF'

P value = 0.00625 (Fisher's exact test), Q value = 0.009

Table S415. Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
2P LOSS MUTATED	57	15	24
2P LOSS WILD-TYPE	172	101	144

Figure S415. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'2p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.036

Table S416. Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
2P LOSS MUTATED	38	49	9
2P LOSS WILD-TYPE	121	217	79

Figure S416. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'2p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S417. Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
2P LOSS MUTATED	92	36	10	43	4
2P LOSS WILD-TYPE	238	96	285	251	25

Figure S417. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #3: 'CN_CNMF'

'2p loss' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S418. Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
2P LOSS MUTATED	51	35	12	12	10
2P LOSS WILD-TYPE	167	148	133	127	78

Figure S418. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2p loss' versus 'RPPA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.037

Table S419. Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
2P LOSS MUTATED	33	56	1	27	20	12	1
2P LOSS WILD-TYPE	161	181	29	177	111	55	9

Figure S419. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'2p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S420. Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
2P LOSS MUTATED	24	96	30
2P LOSS WILD-TYPE	196	302	225

Figure S420. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S421. Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
2P LOSS MUTATED	71	28	16	44	20	2	2
2P LOSS WILD-TYPE	193	141	127	181	183	49	18

Figure S421. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S422. Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
2P LOSS MUTATED	76	43	8	38	16	2
2P LOSS WILD-TYPE	213	120	82	252	167	58

Figure S422. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S423. Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
2P LOSS MUTATED	41	35	40	20	36	9
2P LOSS WILD-TYPE	98	235	168	196	146	37

Figure S423. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00039 (Fisher's exact test), Q value = 7e-04

Table S424. Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
2P LOSS MUTATED	18	23	18	38	16	28	14	13	13
2P LOSS WILD-TYPE	48	100	166	148	58	85	145	60	70

Figure S424. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0018

Table S425. Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
2P LOSS MUTATED	34	7	11	22	14	14
2P LOSS WILD-TYPE	99	85	48	97	131	100

Figure S425. Get High-res Image Gene #44: '2p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'2q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S426. Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
2Q LOSS MUTATED	98	39	11	57	6
2Q LOSS WILD-TYPE	232	93	284	237	23

Figure S426. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #3: 'CN_CNMF'

'2q loss' versus 'METHLYATION_CNMF'

P value = 0.00335 (Fisher's exact test), Q value = 0.005

Table S427. Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
2Q LOSS MUTATED	52	38	15	26	9
2Q LOSS WILD-TYPE	166	145	130	113	79

Figure S427. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'2q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S428. Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
2Q LOSS MUTATED	39	100	31
2Q LOSS WILD-TYPE	181	298	224

Figure S428. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'2q loss' versus 'MRNASEQ_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00074

Table S429. Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
2Q LOSS MUTATED	73	34	17	44	36	3	2
2Q LOSS WILD-TYPE	191	135	126	181	167	48	18

Figure S429. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'2q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S430. Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
2Q LOSS MUTATED	77	46	9	41	32	4
2Q LOSS WILD-TYPE	212	117	81	249	151	56

Figure S430. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0016

Table S431. Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
2Q LOSS MUTATED	42	54	38	24	39	10
2Q LOSS WILD-TYPE	97	216	170	192	143	36

Figure S431. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'2q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.025

Table S432. Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
2Q LOSS MUTATED	18	29	19	38	18	26	31	15	13
2Q LOSS WILD-TYPE	48	94	165	148	56	87	128	58	70

Figure S432. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'2q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00489 (Fisher's exact test), Q value = 0.0071

Table S433. Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
2Q LOSS MUTATED	38	9	12	23	25	14
2Q LOSS WILD-TYPE	95	83	47	96	120	100

Figure S433. Get High-res Image Gene #45: '2q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S434. Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
3P LOSS MUTATED	23	11	53
3P LOSS WILD-TYPE	206	105	115

Figure S434. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S435. Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
3P LOSS MUTATED	11	50	26
3P LOSS WILD-TYPE	148	216	62

Figure S435. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S436. Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
3P LOSS MUTATED	66	16	9	94	3
3P LOSS WILD-TYPE	264	116	286	200	26

Figure S436. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #3: 'CN_CNMF'

'3p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S437. Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
3P LOSS MUTATED	20	47	19	41	5
3P LOSS WILD-TYPE	198	136	126	98	83

Figure S437. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S438. Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
3P LOSS MUTATED	60	21	8	25	26	17	2
3P LOSS WILD-TYPE	134	216	22	179	105	50	8

Figure S438. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S439. Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
3P LOSS MUTATED	69	56	34
3P LOSS WILD-TYPE	151	342	221

Figure S439. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S440. Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
3P LOSS MUTATED	41	50	14	14	59	5	4
3P LOSS WILD-TYPE	223	119	129	211	144	46	16

Figure S440. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S441. Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
3P LOSS MUTATED	31	44	5	36	56	15
3P LOSS WILD-TYPE	258	119	85	254	127	45

Figure S441. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S442. Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
3P LOSS MUTATED	26	80	24	20	23	9
3P LOSS WILD-TYPE	113	190	184	196	159	37

Figure S442. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S443. Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
3P LOSS MUTATED	13	29	16	20	2	18	45	16	23
3P LOSS WILD-TYPE	53	94	168	166	72	95	114	57	60

Figure S443. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'3p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S444. Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
3P LOSS MUTATED	22	10	7	12	48	18
3P LOSS WILD-TYPE	111	82	52	107	97	96

Figure S444. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'3p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.021

Table S445. Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
3P LOSS MUTATED	69	35	13
3P LOSS WILD-TYPE	245	196	104

Figure S445. Get High-res Image Gene #46: '3p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'3q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S446. Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
3Q LOSS MUTATED	13	5	30
3Q LOSS WILD-TYPE	216	111	138

Figure S446. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'3q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.012

Table S447. Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
3Q LOSS MUTATED	6	31	11
3Q LOSS WILD-TYPE	153	235	77

Figure S447. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'3q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S448. Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
3Q LOSS MUTATED	40	11	2	49	3
3Q LOSS WILD-TYPE	290	121	293	245	26

Figure S448. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #3: 'CN_CNMF'

'3q loss' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S449. Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
3Q LOSS MUTATED	14	28	8	24	2
3Q LOSS WILD-TYPE	204	155	137	115	86

Figure S449. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'3q loss' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S450. Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
3Q LOSS MUTATED	35	14	4	11	9	13	1
3Q LOSS WILD-TYPE	159	223	26	193	122	54	9

Figure S450. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'3q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.001

Table S451. Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
3Q LOSS MUTATED	36	36	15
3Q LOSS WILD-TYPE	184	362	240

Figure S451. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'3q loss' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S452. Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
3Q LOSS MUTATED	26	31	7	8	27	4	2
3Q LOSS WILD-TYPE	238	138	136	217	176	47	18

Figure S452. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'3q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00014

Table S453. Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
3Q LOSS MUTATED	21	29	3	18	25	9
3Q LOSS WILD-TYPE	268	134	87	272	158	51

Figure S453. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'3q loss' versus 'MIRSEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.0032

Table S454. Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
3Q LOSS MUTATED	17	40	13	11	14	6
3Q LOSS WILD-TYPE	122	230	195	205	168	40

Figure S454. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'3q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-04 (Fisher's exact test), Q value = 0.00037

Table S455. Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
3Q LOSS MUTATED	11	17	11	8	1	10	22	9	12
3Q LOSS WILD-TYPE	55	106	173	178	73	103	137	64	71

Figure S455. Get High-res Image Gene #47: '3q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S456. Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
4P LOSS MUTATED	55	28	90
4P LOSS WILD-TYPE	174	88	78

Figure S456. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S457. Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
4P LOSS MUTATED	32	87	54
4P LOSS WILD-TYPE	127	179	34

Figure S457. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S458. Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
4P LOSS MUTATED	78	56	26	187	6
4P LOSS WILD-TYPE	252	76	269	107	23

Figure S458. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #3: 'CN_CNMF'

'4p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S459. Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
4P LOSS MUTATED	50	54	35	93	12
4P LOSS WILD-TYPE	168	129	110	46	76

Figure S459. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S460. Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
4P LOSS MUTATED	114	49	7	44	42	31	2
4P LOSS WILD-TYPE	80	188	23	160	89	36	8

Figure S460. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S461. Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
4P LOSS MUTATED	128	101	60
4P LOSS WILD-TYPE	92	297	195

Figure S461. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S462. Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
4P LOSS MUTATED	58	80	16	54	129	7	8
4P LOSS WILD-TYPE	206	89	127	171	74	44	12

Figure S462. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S463. Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
4P LOSS MUTATED	67	69	9	55	120	32
4P LOSS WILD-TYPE	222	94	81	235	63	28

Figure S463. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S464. Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
4P LOSS MUTATED	38	158	31	40	62	13
4P LOSS WILD-TYPE	101	112	177	176	120	33

Figure S464. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S465. Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
4P LOSS MUTATED	17	54	27	40	25	27	102	8	42
4P LOSS WILD-TYPE	49	69	157	146	49	86	57	65	41

Figure S465. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S466. Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
4P LOSS MUTATED	24	21	19	31	96	22
4P LOSS WILD-TYPE	109	71	40	88	49	92

Figure S466. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S467. Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
4P LOSS MUTATED	131	47	35
4P LOSS WILD-TYPE	183	184	82

Figure S467. Get High-res Image Gene #48: '4p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'4q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S468. Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
4Q LOSS MUTATED	51	23	77
4Q LOSS WILD-TYPE	178	93	91

Figure S468. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'4q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S469. Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
4Q LOSS MUTATED	33	77	41
4Q LOSS WILD-TYPE	126	189	47

Figure S469. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'4q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S470. Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
4Q LOSS MUTATED	72	56	22	155	6
4Q LOSS WILD-TYPE	258	76	273	139	23

Figure S470. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #3: 'CN_CNMF'

'4q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S471. Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
4Q LOSS MUTATED	49	49	33	75	12
4Q LOSS WILD-TYPE	169	134	112	64	76

Figure S471. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'4q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S472. Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
4Q LOSS MUTATED	96	42	10	35	43	29	1
4Q LOSS WILD-TYPE	98	195	20	169	88	38	9

Figure S472. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'4q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S473. Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
4Q LOSS MUTATED	106	99	51
4Q LOSS WILD-TYPE	114	299	204

Figure S473. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'4q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S474. Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
4Q LOSS MUTATED	54	73	15	54	102	5	7
4Q LOSS WILD-TYPE	210	96	128	171	101	46	13

Figure S474. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'4q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S475. Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
4Q LOSS MUTATED	63	66	9	51	94	27
4Q LOSS WILD-TYPE	226	97	81	239	89	33

Figure S475. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S476. Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
4Q LOSS MUTATED	34	123	34	37	58	14
4Q LOSS WILD-TYPE	105	147	174	179	124	32

Figure S476. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'4q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S477. Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
4Q LOSS MUTATED	15	43	26	39	26	27	76	8	40
4Q LOSS WILD-TYPE	51	80	158	147	48	86	83	65	43

Figure S477. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'4q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S478. Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
4Q LOSS MUTATED	26	18	18	27	73	20
4Q LOSS WILD-TYPE	107	74	41	92	72	94

Figure S478. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'4q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.00041

Table S479. Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
4Q LOSS MUTATED	106	42	34
4Q LOSS WILD-TYPE	208	189	83

Figure S479. Get High-res Image Gene #49: '4q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S480. Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
5P LOSS MUTATED	14	9	50
5P LOSS WILD-TYPE	215	107	118

Figure S480. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S481. Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
5P LOSS MUTATED	6	30	37
5P LOSS WILD-TYPE	153	236	51

Figure S481. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S482. Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
5P LOSS MUTATED	26	4	6	103	3
5P LOSS WILD-TYPE	304	128	289	191	26

Figure S482. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #3: 'CN_CNMF'

'5p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S483. Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
5P LOSS MUTATED	8	14	20	56	1
5P LOSS WILD-TYPE	210	169	125	83	87

Figure S483. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S484. Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
5P LOSS MUTATED	64	9	1	15	23	13	1
5P LOSS WILD-TYPE	130	228	29	189	108	54	9

Figure S484. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5p loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S485. Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
5P LOSS MUTATED	72	35	19
5P LOSS WILD-TYPE	148	363	236

Figure S485. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S486. Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
5P LOSS MUTATED	20	25	4	7	82	2	1
5P LOSS WILD-TYPE	244	144	139	218	121	49	19

Figure S486. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S487. Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
5P LOSS MUTATED	14	25	1	12	78	11
5P LOSS WILD-TYPE	275	138	89	278	105	49

Figure S487. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S488. Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
5P LOSS MUTATED	19	81	3	16	14	6
5P LOSS WILD-TYPE	120	189	205	200	168	40

Figure S488. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S489. Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
5P LOSS MUTATED	8	20	3	7	4	9	69	5	14
5P LOSS WILD-TYPE	58	103	181	179	70	104	90	68	69

Figure S489. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S490. Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
5P LOSS MUTATED	10	3	2	6	57	7
5P LOSS WILD-TYPE	123	89	57	113	88	107

Figure S490. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S491. Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
5P LOSS MUTATED	73	8	4
5P LOSS WILD-TYPE	241	223	113

Figure S491. Get High-res Image Gene #50: '5p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'5q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S492. Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
5Q LOSS MUTATED	16	16	79
5Q LOSS WILD-TYPE	213	100	89

Figure S492. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'5q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S493. Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
5Q LOSS MUTATED	7	49	55
5Q LOSS WILD-TYPE	152	217	33

Figure S493. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'5q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S494. Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
5Q LOSS MUTATED	34	7	8	175	4
5Q LOSS WILD-TYPE	296	125	287	119	25

Figure S494. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #3: 'CN_CNMF'

'5q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S495. Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
5Q LOSS MUTATED	13	22	32	93	3
5Q LOSS WILD-TYPE	205	161	113	46	85

Figure S495. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'5q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S496. Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
5Q LOSS MUTATED	98	13	6	23	34	24	2
5Q LOSS WILD-TYPE	96	224	24	181	97	43	8

Figure S496. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'5q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S497. Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
5Q LOSS MUTATED	116	53	31
5Q LOSS WILD-TYPE	104	345	224

Figure S497. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'5q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S498. Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
5Q LOSS MUTATED	34	42	7	8	128	3	5
5Q LOSS WILD-TYPE	230	127	136	217	75	48	15

Figure S498. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'5q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S499. Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
5Q LOSS MUTATED	23	38	1	23	121	21
5Q LOSS WILD-TYPE	266	125	89	267	62	39

Figure S499. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S500. Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
5Q LOSS MUTATED	28	145	5	18	19	8
5Q LOSS WILD-TYPE	111	125	203	198	163	38

Figure S500. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'5q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S501. Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
5Q LOSS MUTATED	10	39	4	10	5	11	106	7	31
5Q LOSS WILD-TYPE	56	84	180	176	69	102	53	66	52

Figure S501. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'5q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S502. Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
5Q LOSS MUTATED	16	10	4	8	92	11
5Q LOSS WILD-TYPE	117	82	55	111	53	103

Figure S502. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'5q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S503. Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
5Q LOSS MUTATED	114	19	8
5Q LOSS WILD-TYPE	200	212	109

Figure S503. Get High-res Image Gene #51: '5q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'6p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0477 (Fisher's exact test), Q value = 0.058

Table S504. Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
6P LOSS MUTATED	36	51	9
6P LOSS WILD-TYPE	123	215	79

Figure S504. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S505. Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
6P LOSS MUTATED	103	27	26	29	5
6P LOSS WILD-TYPE	227	105	269	265	24

Figure S505. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #3: 'CN_CNMF'

'6p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00652 (Fisher's exact test), Q value = 0.0093

Table S506. Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
6P LOSS MUTATED	28	89	40
6P LOSS WILD-TYPE	192	309	215

Figure S506. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6p loss' versus 'MRNASEQ_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.0047

Table S507. Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
6P LOSS MUTATED	65	31	23	41	21	7	1
6P LOSS WILD-TYPE	199	138	120	184	182	44	19

Figure S507. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00882 (Fisher's exact test), Q value = 0.012

Table S508. Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
6P LOSS MUTATED	68	30	15	48	18	10
6P LOSS WILD-TYPE	221	133	75	242	165	50

Figure S508. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00628 (Fisher's exact test), Q value = 0.009

Table S509. Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
6P LOSS MUTATED	17	19	26	43	17	24	15	16	11
6P LOSS WILD-TYPE	49	104	158	143	57	89	144	57	72

Figure S509. Get High-res Image Gene #52: '6p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.032

Table S510. Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
6Q LOSS MUTATED	47	72	13
6Q LOSS WILD-TYPE	112	194	75

Figure S510. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'6q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S511. Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
6Q LOSS MUTATED	149	39	45	37	10
6Q LOSS WILD-TYPE	181	93	250	257	19

Figure S511. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #3: 'CN_CNMF'

'6q loss' versus 'METHLYATION_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0016

Table S512. Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
6Q LOSS MUTATED	73	57	28	26	17
6Q LOSS WILD-TYPE	145	126	117	113	71

Figure S512. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'6q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0013

Table S513. Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
6Q LOSS MUTATED	40	127	62
6Q LOSS WILD-TYPE	180	271	193

Figure S513. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'6q loss' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S514. Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
6Q LOSS MUTATED	98	43	37	58	30	11	2
6Q LOSS WILD-TYPE	166	126	106	167	173	40	18

Figure S514. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'6q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.00067

Table S515. Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
6Q LOSS MUTATED	94	42	23	78	25	17
6Q LOSS WILD-TYPE	195	121	67	212	158	43

Figure S515. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_CNMF'

P value = 0.00786 (Fisher's exact test), Q value = 0.011

Table S516. Gene #53: '6q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
6Q LOSS MUTATED	43	52	67	53	46	17
6Q LOSS WILD-TYPE	96	218	141	163	136	29

Figure S516. 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 = 4.5e-05

Table S517. Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
6Q LOSS MUTATED	25	27	43	62	27	36	21	22	15
6Q LOSS WILD-TYPE	41	96	141	124	47	77	138	51	68

Figure S517. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'6q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.014

Table S518. Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
6Q LOSS MUTATED	40	19	21	35	23	33
6Q LOSS WILD-TYPE	93	73	38	84	122	81

Figure S518. Get High-res Image Gene #53: '6q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MRNA_CNMF'

P value = 0.00559 (Fisher's exact test), Q value = 0.0081

Table S519. Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
7P LOSS MUTATED	24	6	29
7P LOSS WILD-TYPE	205	110	139

Figure S519. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'7p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S520. Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
7P LOSS MUTATED	46	9	5	51	0
7P LOSS WILD-TYPE	284	123	290	243	29

Figure S520. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #3: 'CN_CNMF'

'7p loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S521. Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
7P LOSS MUTATED	12	23	6	28	2
7P LOSS WILD-TYPE	206	160	139	111	86

Figure S521. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7p loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S522. Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
7P LOSS MUTATED	37	17	5	12	10	10	0
7P LOSS WILD-TYPE	157	220	25	192	121	57	10

Figure S522. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.01

Table S523. Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
7P LOSS MUTATED	33	42	16
7P LOSS WILD-TYPE	187	356	239

Figure S523. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'7p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S524. Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
7P LOSS MUTATED	33	22	4	10	35	2	4
7P LOSS WILD-TYPE	231	147	139	215	168	49	16

Figure S524. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S525. Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
7P LOSS MUTATED	31	25	0	19	29	6
7P LOSS WILD-TYPE	258	138	90	271	154	54

Figure S525. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S526. Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
7P LOSS MUTATED	18	47	20	4	16	4
7P LOSS WILD-TYPE	121	223	188	212	166	42

Figure S526. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S527. Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
7P LOSS MUTATED	9	16	6	15	3	15	27	4	14
7P LOSS WILD-TYPE	57	107	178	171	71	98	132	69	69

Figure S527. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S528. Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
7P LOSS MUTATED	15	5	3	7	29	2
7P LOSS WILD-TYPE	118	87	56	112	116	112

Figure S528. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00243 (Fisher's exact test), Q value = 0.0038

Table S529. Gene #54: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
7P LOSS MUTATED	42	13	6
7P LOSS WILD-TYPE	272	218	111

Figure S529. Get High-res Image Gene #54: '7p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'7q loss' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S530. Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
7Q LOSS MUTATED	54	14	13	39	0
7Q LOSS WILD-TYPE	276	118	282	255	29

Figure S530. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #3: 'CN_CNMF'

'7q loss' versus 'METHLYATION_CNMF'

P value = 0.00334 (Fisher's exact test), Q value = 0.005

Table S531. Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
7Q LOSS MUTATED	17	27	6	19	5
7Q LOSS WILD-TYPE	201	156	139	120	83

Figure S531. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'7q loss' versus 'RPPA_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.033

Table S532. Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
7Q LOSS MUTATED	26	23	3	15	14	16	1
7Q LOSS WILD-TYPE	168	214	27	189	117	51	9

Figure S532. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'7q loss' versus 'MRNASEQ_CNMF'

P value = 0.00171 (Fisher's exact test), Q value = 0.0027

Table S533. Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
7Q LOSS MUTATED	32	30	6	20	22	4	5
7Q LOSS WILD-TYPE	232	139	137	205	181	47	15

Figure S533. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'7q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S534. Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
7Q LOSS MUTATED	39	31	2	24	16	7
7Q LOSS WILD-TYPE	250	132	88	266	167	53

Figure S534. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0012

Table S535. Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
7Q LOSS MUTATED	22	38	23	8	21	6
7Q LOSS WILD-TYPE	117	232	185	208	161	40

Figure S535. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'7q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.00029

Table S536. Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
7Q LOSS MUTATED	11	23	6	19	6	17	15	6	15
7Q LOSS WILD-TYPE	55	100	178	167	68	96	144	67	68

Figure S536. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'7q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00968 (Fisher's exact test), Q value = 0.013

Table S537. Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
7Q LOSS MUTATED	17	6	6	12	22	3
7Q LOSS WILD-TYPE	116	86	53	107	123	111

Figure S537. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'7q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.022

Table S538. Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
7Q LOSS MUTATED	40	13	13
7Q LOSS WILD-TYPE	274	218	104

Figure S538. Get High-res Image Gene #55: '7q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8p loss' versus 'MRNA_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.026

Table S539. Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
8P LOSS MUTATED	79	41	80
8P LOSS WILD-TYPE	150	75	88

Figure S539. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'8p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S540. Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
8P LOSS MUTATED	156	23	61	148	7
8P LOSS WILD-TYPE	174	109	234	146	22

Figure S540. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #3: 'CN_CNMF'

'8p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S541. Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
8P LOSS MUTATED	61	85	49	60	15
8P LOSS WILD-TYPE	157	98	96	79	73

Figure S541. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'8p loss' versus 'RPPA_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S542. Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
8P LOSS MUTATED	88	74	12	60	53	37	6
8P LOSS WILD-TYPE	106	163	18	144	78	30	4

Figure S542. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'8p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.04

Table S543. Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
8P LOSS MUTATED	99	145	86
8P LOSS WILD-TYPE	121	253	169

Figure S543. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'8p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S544. Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
8P LOSS MUTATED	113	87	36	44	82	18	12
8P LOSS WILD-TYPE	151	82	107	181	121	33	8

Figure S544. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S545. Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
8P LOSS MUTATED	98	80	19	89	72	34
8P LOSS WILD-TYPE	191	83	71	201	111	26

Figure S545. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S546. Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
8P LOSS MUTATED	61	127	65	53	66	17
8P LOSS WILD-TYPE	78	143	143	163	116	29

Figure S546. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'8p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S547. Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
8P LOSS MUTATED	29	53	45	55	26	40	65	30	46
8P LOSS WILD-TYPE	37	70	139	131	48	73	94	43	37

Figure S547. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'8p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.0037

Table S548. Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
8P LOSS MUTATED	133	75	30
8P LOSS WILD-TYPE	181	156	87

Figure S548. Get High-res Image Gene #56: '8p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'8q loss' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S549. Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
8Q LOSS MUTATED	47	10	10	25	1
8Q LOSS WILD-TYPE	283	122	285	269	28

Figure S549. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #3: 'CN_CNMF'

'8q loss' versus 'MRNASEQ_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.013

Table S550. Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
8Q LOSS MUTATED	26	27	6	17	14	2	1
8Q LOSS WILD-TYPE	238	142	137	208	189	49	19

Figure S550. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'8q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.02

Table S551. Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
8Q LOSS MUTATED	29	18	1	22	14	9
8Q LOSS WILD-TYPE	260	145	89	268	169	51

Figure S551. Get High-res Image Gene #57: '8q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MRNA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S552. Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
9P LOSS MUTATED	69	22	74
9P LOSS WILD-TYPE	160	94	94

Figure S552. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0402 (Fisher's exact test), Q value = 0.049

Table S553. Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
9P LOSS MUTATED	42	99	24
9P LOSS WILD-TYPE	117	167	64

Figure S553. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S554. Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
9P LOSS MUTATED	169	14	17	106	7
9P LOSS WILD-TYPE	161	118	278	188	22

Figure S554. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #3: 'CN_CNMF'

'9p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S555. Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
9P LOSS MUTATED	54	73	24	49	10
9P LOSS WILD-TYPE	164	110	121	90	78

Figure S555. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9p loss' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 1e-04

Table S556. Gene #58: '9p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
9P LOSS MUTATED	74	52	11	50	38	28	7
9P LOSS WILD-TYPE	120	185	19	154	93	39	3

Figure S556. 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 = 2.3e-05

Table S557. Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
9P LOSS MUTATED	111	72	17	38	57	8	8
9P LOSS WILD-TYPE	153	97	126	187	146	43	12

Figure S557. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S558. Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
9P LOSS MUTATED	96	76	5	59	49	26
9P LOSS WILD-TYPE	193	87	85	231	134	34

Figure S558. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S559. Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
9P LOSS MUTATED	68	103	46	27	51	12
9P LOSS WILD-TYPE	71	167	162	189	131	34

Figure S559. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S560. Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
9P LOSS MUTATED	27	52	19	47	19	40	44	18	41
9P LOSS WILD-TYPE	39	71	165	139	55	73	115	55	42

Figure S560. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.00027

Table S561. Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
9P LOSS MUTATED	51	19	14	23	56	23
9P LOSS WILD-TYPE	82	73	45	96	89	91

Figure S561. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S562. Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
9P LOSS MUTATED	120	47	19
9P LOSS WILD-TYPE	194	184	98

Figure S562. Get High-res Image Gene #58: '9p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'9q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S563. Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
9Q LOSS MUTATED	57	18	71
9Q LOSS WILD-TYPE	172	98	97

Figure S563. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'9q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.028

Table S564. Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
9Q LOSS MUTATED	35	77	34
9Q LOSS WILD-TYPE	124	189	54

Figure S564. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'9q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S565. Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
9Q LOSS MUTATED	136	12	13	111	8
9Q LOSS WILD-TYPE	194	120	282	183	21

Figure S565. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #3: 'CN_CNMF'

'9q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S566. Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
9Q LOSS MUTATED	47	53	24	58	7
9Q LOSS WILD-TYPE	171	130	121	81	81

Figure S566. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'9q loss' versus 'RPPA_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S567. Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
9Q LOSS MUTATED	71	43	11	38	35	23	5
9Q LOSS WILD-TYPE	123	194	19	166	96	44	5

Figure S567. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'9q loss' versus 'RPPA_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S568. Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
9Q LOSS MUTATED	80	98	48
9Q LOSS WILD-TYPE	140	300	207

Figure S568. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'9q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S569. Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
9Q LOSS MUTATED	93	48	11	38	75	5	8
9Q LOSS WILD-TYPE	171	121	132	187	128	46	12

Figure S569. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'9q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S570. Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
9Q LOSS MUTATED	81	61	3	47	66	20
9Q LOSS WILD-TYPE	208	102	87	243	117	40

Figure S570. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S571. Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
9Q LOSS MUTATED	53	111	38	22	38	9
9Q LOSS WILD-TYPE	86	159	170	194	144	37

Figure S571. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'9q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S572. Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
9Q LOSS MUTATED	18	47	15	35	15	37	58	14	32
9Q LOSS WILD-TYPE	48	76	169	151	59	76	101	59	51

Figure S572. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'9q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S573. Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
9Q LOSS MUTATED	43	17	10	16	59	18
9Q LOSS WILD-TYPE	90	75	49	103	86	96

Figure S573. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'9q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S574. Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
9Q LOSS MUTATED	110	41	12
9Q LOSS WILD-TYPE	204	190	105

Figure S574. Get High-res Image Gene #59: '9q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'10p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S575. Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
10P LOSS MUTATED	71	20	14	66	4
10P LOSS WILD-TYPE	259	112	281	228	25

Figure S575. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #3: 'CN_CNMF'

'10p loss' versus 'METHLYATION_CNMF'

P value = 0.00062 (Fisher's exact test), Q value = 0.0011

Table S576. Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
10P LOSS MUTATED	39	37	11	33	9
10P LOSS WILD-TYPE	179	146	134	106	79

Figure S576. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10p loss' versus 'MRNASEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S577. Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
10P LOSS MUTATED	52	41	10	27	39	4	2
10P LOSS WILD-TYPE	212	128	133	198	164	47	18

Figure S577. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S578. Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
10P LOSS MUTATED	51	42	4	33	33	12
10P LOSS WILD-TYPE	238	121	86	257	150	48

Figure S578. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10p loss' versus 'MIRSEQ_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S579. Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
10P LOSS MUTATED	35	53	33	16	28	7
10P LOSS WILD-TYPE	104	217	175	200	154	39

Figure S579. Get High-res Image Gene #60: '10p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MRNA_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S580. Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
10Q LOSS MUTATED	37	17	55
10Q LOSS WILD-TYPE	192	99	113

Figure S580. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'10q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.014 (Fisher's exact test), Q value = 0.019

Table S581. Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
10Q LOSS MUTATED	25	56	28
10Q LOSS WILD-TYPE	134	210	60

Figure S581. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'10q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S582. Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
10Q LOSS MUTATED	84	23	15	102	7
10Q LOSS WILD-TYPE	246	109	280	192	22

Figure S582. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #3: 'CN_CNMF'

'10q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S583. Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
10Q LOSS MUTATED	42	50	17	55	10
10Q LOSS WILD-TYPE	176	133	128	84	78

Figure S583. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'10q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S584. Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
10Q LOSS MUTATED	63	39	11	27	38	20	2
10Q LOSS WILD-TYPE	131	198	19	177	93	47	8

Figure S584. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'10q loss' versus 'RPPA_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S585. Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
10Q LOSS MUTATED	74	84	42
10Q LOSS WILD-TYPE	146	314	213

Figure S585. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'10q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S586. Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
10Q LOSS MUTATED	64	53	12	28	69	2	3
10Q LOSS WILD-TYPE	200	116	131	197	134	49	17

Figure S586. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'10q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S587. Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
10Q LOSS MUTATED	56	55	4	39	62	15
10Q LOSS WILD-TYPE	233	108	86	251	121	45

Figure S587. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S588. Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
10Q LOSS MUTATED	42	83	33	23	38	7
10Q LOSS WILD-TYPE	97	187	175	193	144	39

Figure S588. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'10q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S589. Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
10Q LOSS MUTATED	20	36	21	26	10	23	48	13	29
10Q LOSS WILD-TYPE	46	87	163	160	64	90	111	60	54

Figure S589. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'10q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0053 (Fisher's exact test), Q value = 0.0077

Table S590. Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
10Q LOSS MUTATED	32	16	12	20	49	18
10Q LOSS WILD-TYPE	101	76	47	99	96	96

Figure S590. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'10q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00079 (Fisher's exact test), Q value = 0.0013

Table S591. Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
10Q LOSS MUTATED	90	39	18
10Q LOSS WILD-TYPE	224	192	99

Figure S591. Get High-res Image Gene #61: '10q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S592. Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
11P LOSS MUTATED	120	25	15	105	5
11P LOSS WILD-TYPE	210	107	280	189	24

Figure S592. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #3: 'CN_CNMF'

'11p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S593. Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
11P LOSS MUTATED	40	64	22	52	8
11P LOSS WILD-TYPE	178	119	123	87	80

Figure S593. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'11p loss' versus 'RPPA_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.0048

Table S594. Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
11P LOSS MUTATED	64	52	9	36	40	18	5
11P LOSS WILD-TYPE	130	185	21	168	91	49	5

Figure S594. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'11p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00333 (Fisher's exact test), Q value = 0.005

Table S595. Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
11P LOSS MUTATED	72	103	49
11P LOSS WILD-TYPE	148	295	206

Figure S595. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'11p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S596. Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
11P LOSS MUTATED	86	58	20	26	63	11	6
11P LOSS WILD-TYPE	178	111	123	199	140	40	14

Figure S596. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S597. Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
11P LOSS MUTATED	74	61	7	52	57	19
11P LOSS WILD-TYPE	215	102	83	238	126	41

Figure S597. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S598. Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
11P LOSS MUTATED	41	94	41	37	40	9
11P LOSS WILD-TYPE	98	176	167	179	142	37

Figure S598. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S599. Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
11P LOSS MUTATED	23	40	21	40	17	29	49	17	26
11P LOSS WILD-TYPE	43	83	163	146	57	84	110	56	57

Figure S599. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'11p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.023

Table S600. Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
11P LOSS MUTATED	34	14	13	26	50	23
11P LOSS WILD-TYPE	99	78	46	93	95	91

Figure S600. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'11p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.031

Table S601. Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
11P LOSS MUTATED	91	45	24
11P LOSS WILD-TYPE	223	186	93

Figure S601. Get High-res Image Gene #62: '11p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'11q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S602. Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
11Q LOSS MUTATED	190	36	34	101	5
11Q LOSS WILD-TYPE	140	96	261	193	24

Figure S602. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #3: 'CN_CNMF'

'11q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S603. Gene #63: '11q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
11Q LOSS MUTATED	73	85	31	50	19
11Q LOSS WILD-TYPE	145	98	114	89	69

Figure S603. 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 = 2.3e-05

Table S604. Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
11Q LOSS MUTATED	140	58	39	47	59	17	4
11Q LOSS WILD-TYPE	124	111	104	178	144	34	16

Figure S604. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'11q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00299 (Fisher's exact test), Q value = 0.0046

Table S605. Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
11Q LOSS MUTATED	115	66	18	93	54	18
11Q LOSS WILD-TYPE	174	97	72	197	129	42

Figure S605. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'11q loss' versus 'MIRSEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.033

Table S606. Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
11Q LOSS MUTATED	60	93	76	57	60	12
11Q LOSS WILD-TYPE	79	177	132	159	122	34

Figure S606. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'11q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00823 (Fisher's exact test), Q value = 0.011

Table S607. Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
11Q LOSS MUTATED	28	45	40	69	25	47	48	26	30
11Q LOSS WILD-TYPE	38	78	144	117	49	66	111	47	53

Figure S607. Get High-res Image Gene #63: '11q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MRNA_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.00032

Table S608. Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
12P LOSS MUTATED	21	14	40
12P LOSS WILD-TYPE	208	102	128

Figure S608. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00165 (Fisher's exact test), Q value = 0.0027

Table S609. Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
12P LOSS MUTATED	14	38	23
12P LOSS WILD-TYPE	145	228	65

Figure S609. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S610. Gene #64: '12p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
12P LOSS MUTATED	44	17	19	72	1
12P LOSS WILD-TYPE	286	115	276	222	28

Figure S610. 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 = 2.3e-05

Table S611. Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
12P LOSS MUTATED	20	22	14	42	9
12P LOSS WILD-TYPE	198	161	131	97	79

Figure S611. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S612. Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
12P LOSS MUTATED	34	20	8	18	25	20	2
12P LOSS WILD-TYPE	160	217	22	186	106	47	8

Figure S612. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12p loss' versus 'RPPA_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S613. Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
12P LOSS MUTATED	54	46	27
12P LOSS WILD-TYPE	166	352	228

Figure S613. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S614. Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
12P LOSS MUTATED	31	27	10	19	59	3	3
12P LOSS WILD-TYPE	233	142	133	206	144	48	17

Figure S614. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S615. Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
12P LOSS MUTATED	29	26	6	26	50	15
12P LOSS WILD-TYPE	260	137	84	264	133	45

Figure S615. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S616. Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
12P LOSS MUTATED	26	65	12	16	25	7
12P LOSS WILD-TYPE	113	205	196	200	157	39

Figure S616. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S617. Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
12P LOSS MUTATED	7	23	11	21	7	14	42	10	16
12P LOSS WILD-TYPE	59	100	173	165	67	99	117	63	67

Figure S617. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S618. Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
12P LOSS MUTATED	16	8	7	12	46	7
12P LOSS WILD-TYPE	117	84	52	107	99	107

Figure S618. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S619. Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
12P LOSS MUTATED	70	16	10
12P LOSS WILD-TYPE	244	215	107

Figure S619. Get High-res Image Gene #64: '12p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'12q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S620. Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
12Q LOSS MUTATED	11	16	38
12Q LOSS WILD-TYPE	218	100	130

Figure S620. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'12q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S621. Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
12Q LOSS MUTATED	7	28	30
12Q LOSS WILD-TYPE	152	238	58

Figure S621. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'12q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S622. Gene #65: '12q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
12Q LOSS MUTATED	27	14	10	85	1
12Q LOSS WILD-TYPE	303	118	285	209	28

Figure S622. 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 = 2.3e-05

Table S623. Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
12Q LOSS MUTATED	13	19	11	54	4
12Q LOSS WILD-TYPE	205	164	134	85	84

Figure S623. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'12q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S624. Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
12Q LOSS MUTATED	43	13	5	13	21	14	2
12Q LOSS WILD-TYPE	151	224	25	191	110	53	8

Figure S624. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'12q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S625. Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
12Q LOSS MUTATED	56	36	19
12Q LOSS WILD-TYPE	164	362	236

Figure S625. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'12q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S626. Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
12Q LOSS MUTATED	19	20	7	13	73	3	1
12Q LOSS WILD-TYPE	245	149	136	212	130	48	19

Figure S626. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'12q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S627. Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
12Q LOSS MUTATED	17	18	4	20	64	13
12Q LOSS WILD-TYPE	272	145	86	270	119	47

Figure S627. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S628. Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
12Q LOSS MUTATED	18	74	7	16	13	6
12Q LOSS WILD-TYPE	121	196	201	200	169	40

Figure S628. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'12q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S629. Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
12Q LOSS MUTATED	5	15	7	11	6	12	54	8	16
12Q LOSS WILD-TYPE	61	108	177	175	68	101	105	65	67

Figure S629. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'12q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S630. Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
12Q LOSS MUTATED	11	6	7	12	53	7
12Q LOSS WILD-TYPE	122	86	52	107	92	107

Figure S630. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'12q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S631. Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
12Q LOSS MUTATED	72	16	8
12Q LOSS WILD-TYPE	242	215	109

Figure S631. Get High-res Image Gene #65: '12q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'13q loss' versus 'MRNA_CNMF'

P value = 0.0015 (Fisher's exact test), Q value = 0.0024

Table S632. Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
13Q LOSS MUTATED	93	36	88
13Q LOSS WILD-TYPE	136	80	80

Figure S632. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'13q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S633. Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
13Q LOSS MUTATED	174	61	35	146	14
13Q LOSS WILD-TYPE	156	71	260	148	15

Figure S633. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #3: 'CN_CNMF'

'13q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S634. Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
13Q LOSS MUTATED	86	84	42	75	14
13Q LOSS WILD-TYPE	132	99	103	64	74

Figure S634. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'13q loss' versus 'RPPA_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.0064

Table S635. Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
13Q LOSS MUTATED	102	87	13	69	56	27	2
13Q LOSS WILD-TYPE	92	150	17	135	75	40	8

Figure S635. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'13q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.00083

Table S636. Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
13Q LOSS MUTATED	115	147	94
13Q LOSS WILD-TYPE	105	251	161

Figure S636. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'13q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S637. Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
13Q LOSS MUTATED	115	81	38	65	105	14	11
13Q LOSS WILD-TYPE	149	88	105	160	98	37	9

Figure S637. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'13q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S638. Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
13Q LOSS MUTATED	118	82	18	91	96	24
13Q LOSS WILD-TYPE	171	81	72	199	87	36

Figure S638. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S639. Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
13Q LOSS MUTATED	64	135	84	54	68	18
13Q LOSS WILD-TYPE	75	135	124	162	114	28

Figure S639. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'13q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S640. Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
13Q LOSS MUTATED	24	63	41	73	20	55	79	30	38
13Q LOSS WILD-TYPE	42	60	143	113	54	58	80	43	45

Figure S640. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'13q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.00091

Table S641. Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
13Q LOSS MUTATED	55	25	18	40	75	34
13Q LOSS WILD-TYPE	78	67	41	79	70	80

Figure S641. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'13q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00067 (Fisher's exact test), Q value = 0.0011

Table S642. Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
13Q LOSS MUTATED	141	71	35
13Q LOSS WILD-TYPE	173	160	82

Figure S642. Get High-res Image Gene #66: '13q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'14q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S643. Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
14Q LOSS MUTATED	35	20	66
14Q LOSS WILD-TYPE	194	96	102

Figure S643. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'14q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S644. Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
14Q LOSS MUTATED	18	56	47
14Q LOSS WILD-TYPE	141	210	41

Figure S644. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'14q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S645. Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
14Q LOSS MUTATED	74	21	11	156	7
14Q LOSS WILD-TYPE	256	111	284	138	22

Figure S645. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #3: 'CN_CNMF'

'14q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S646. Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
14Q LOSS MUTATED	27	45	31	88	7
14Q LOSS WILD-TYPE	191	138	114	51	81

Figure S646. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'14q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S647. Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
14Q LOSS MUTATED	93	29	6	40	30	19	2
14Q LOSS WILD-TYPE	101	208	24	164	101	48	8

Figure S647. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'14q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S648. Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
14Q LOSS MUTATED	93	69	57
14Q LOSS WILD-TYPE	127	329	198

Figure S648. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'14q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S649. Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
14Q LOSS MUTATED	66	42	14	17	115	7	7
14Q LOSS WILD-TYPE	198	127	129	208	88	44	13

Figure S649. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'14q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S650. Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
14Q LOSS MUTATED	42	56	3	45	110	12
14Q LOSS WILD-TYPE	247	107	87	245	73	48

Figure S650. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S651. Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
14Q LOSS MUTATED	34	136	31	31	26	4
14Q LOSS WILD-TYPE	105	134	177	185	156	42

Figure S651. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'14q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S652. Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
14Q LOSS MUTATED	14	35	20	24	9	22	92	12	34
14Q LOSS WILD-TYPE	52	88	164	162	65	91	67	61	49

Figure S652. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'14q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S653. Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
14Q LOSS MUTATED	23	20	13	17	82	18
14Q LOSS WILD-TYPE	110	72	46	102	63	96

Figure S653. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'14q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S654. Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
14Q LOSS MUTATED	114	39	20
14Q LOSS WILD-TYPE	200	192	97

Figure S654. Get High-res Image Gene #67: '14q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'15q loss' versus 'MRNA_CNMF'

P value = 7e-04 (Fisher's exact test), Q value = 0.0012

Table S655. Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
15Q LOSS MUTATED	60	26	70
15Q LOSS WILD-TYPE	169	90	98

Figure S655. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'15q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.00039

Table S656. Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
15Q LOSS MUTATED	35	79	42
15Q LOSS WILD-TYPE	124	187	46

Figure S656. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'15q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S657. Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
15Q LOSS MUTATED	94	55	14	148	7
15Q LOSS WILD-TYPE	236	77	281	146	22

Figure S657. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #3: 'CN_CNMF'

'15q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S658. Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
15Q LOSS MUTATED	46	59	32	81	10
15Q LOSS WILD-TYPE	172	124	113	58	78

Figure S658. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'15q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S659. Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
15Q LOSS MUTATED	89	58	14	33	47	28	2
15Q LOSS WILD-TYPE	105	179	16	171	84	39	8

Figure S659. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'15q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S660. Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
15Q LOSS MUTATED	101	116	54
15Q LOSS WILD-TYPE	119	282	201

Figure S660. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'15q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S661. Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
15Q LOSS MUTATED	73	70	16	47	99	4	6
15Q LOSS WILD-TYPE	191	99	127	178	104	47	14

Figure S661. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'15q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S662. Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
15Q LOSS MUTATED	73	65	8	57	95	17
15Q LOSS WILD-TYPE	216	98	82	233	88	43

Figure S662. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S663. Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
15Q LOSS MUTATED	43	126	37	30	56	18
15Q LOSS WILD-TYPE	96	144	171	186	126	28

Figure S663. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'15q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S664. Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
15Q LOSS MUTATED	17	42	22	33	28	35	81	11	41
15Q LOSS WILD-TYPE	49	81	162	153	46	78	78	62	42

Figure S664. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'15q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S665. Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
15Q LOSS MUTATED	39	22	20	21	75	15
15Q LOSS WILD-TYPE	94	70	39	98	70	99

Figure S665. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'15q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S666. Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
15Q LOSS MUTATED	122	41	29
15Q LOSS WILD-TYPE	192	190	88

Figure S666. Get High-res Image Gene #68: '15q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'16p loss' versus 'CN_CNMF'

P value = 0.00336 (Fisher's exact test), Q value = 0.005

Table S667. Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
16P LOSS MUTATED	46	15	39	68	6
16P LOSS WILD-TYPE	284	117	256	226	23

Figure S667. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #3: 'CN_CNMF'

'16p loss' versus 'METHLYATION_CNMF'

P value = 0.00041 (Fisher's exact test), Q value = 0.00074

Table S668. Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
16P LOSS MUTATED	24	27	25	40	10
16P LOSS WILD-TYPE	194	156	120	99	78

Figure S668. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16p loss' versus 'RPPA_CNMF'

P value = 0.00046 (Fisher's exact test), Q value = 0.00082

Table S669. Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
16P LOSS MUTATED	53	37	4	24	17	5	2
16P LOSS WILD-TYPE	141	200	26	180	114	62	8

Figure S669. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'16p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00247 (Fisher's exact test), Q value = 0.0038

Table S670. Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
16P LOSS MUTATED	51	62	29
16P LOSS WILD-TYPE	169	336	226

Figure S670. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16p loss' versus 'MRNASEQ_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S671. Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
16P LOSS MUTATED	38	26	17	29	56	3	4
16P LOSS WILD-TYPE	226	143	126	196	147	48	16

Figure S671. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00225 (Fisher's exact test), Q value = 0.0035

Table S672. Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
16P LOSS MUTATED	38	24	13	40	50	8
16P LOSS WILD-TYPE	251	139	77	250	133	52

Figure S672. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.00023

Table S673. Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
16P LOSS MUTATED	20	67	27	26	20	12
16P LOSS WILD-TYPE	119	203	181	190	162	34

Figure S673. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00434 (Fisher's exact test), Q value = 0.0064

Table S674. Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
16P LOSS MUTATED	6	17	26	24	14	17	45	8	15
16P LOSS WILD-TYPE	60	106	158	162	60	96	114	65	68

Figure S674. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S675. Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
16P LOSS MUTATED	16	13	4	12	44	20
16P LOSS WILD-TYPE	117	79	55	107	101	94

Figure S675. Get High-res Image Gene #69: '16p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S676. Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
16Q LOSS MUTATED	149	69	64
16Q LOSS WILD-TYPE	80	47	104

Figure S676. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'16q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S677. Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
16Q LOSS MUTATED	105	154	23
16Q LOSS WILD-TYPE	54	112	65

Figure S677. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'16q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S678. Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
16Q LOSS MUTATED	169	94	180	125	23
16Q LOSS WILD-TYPE	161	38	115	169	6

Figure S678. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #3: 'CN_CNMF'

'16q loss' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00022

Table S679. Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
16Q LOSS MUTATED	136	107	68	56	54
16Q LOSS WILD-TYPE	82	76	77	83	34

Figure S679. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'16q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S680. Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
16Q LOSS MUTATED	83	239	151
16Q LOSS WILD-TYPE	137	159	104

Figure S680. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'16q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S681. Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
16Q LOSS MUTATED	127	82	94	171	70	35	10
16Q LOSS WILD-TYPE	137	87	49	54	133	16	10

Figure S681. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'16q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S682. Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
16Q LOSS MUTATED	164	85	65	195	63	17
16Q LOSS WILD-TYPE	125	78	25	95	120	43

Figure S682. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S683. Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
16Q LOSS MUTATED	66	104	128	131	113	39
16Q LOSS WILD-TYPE	73	166	80	85	69	7

Figure S683. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'16q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S684. Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
16Q LOSS MUTATED	23	58	129	106	64	75	57	40	29
16Q LOSS WILD-TYPE	43	65	55	80	10	38	102	33	54

Figure S684. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'16q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0011 (Fisher's exact test), Q value = 0.0018

Table S685. Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
16Q LOSS MUTATED	69	60	28	71	61	73
16Q LOSS WILD-TYPE	64	32	31	48	84	41

Figure S685. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'16q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S686. Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
16Q LOSS MUTATED	140	148	74
16Q LOSS WILD-TYPE	174	83	43

Figure S686. Get High-res Image Gene #70: '16q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'17p loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S687. Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
17P LOSS MUTATED	100	64	118
17P LOSS WILD-TYPE	129	52	50

Figure S687. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17p loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S688. Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
17P LOSS MUTATED	62	167	53
17P LOSS WILD-TYPE	97	99	35

Figure S688. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S689. Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
17P LOSS MUTATED	201	69	86	210	14
17P LOSS WILD-TYPE	129	63	209	84	15

Figure S689. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #3: 'CN_CNMF'

'17p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S690. Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
17P LOSS MUTATED	103	119	58	89	35
17P LOSS WILD-TYPE	115	64	87	50	53

Figure S690. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17p loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S691. Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
17P LOSS MUTATED	132	105	23	82	81	46	5
17P LOSS WILD-TYPE	62	132	7	122	50	21	5

Figure S691. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17p loss' versus 'RPPA_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S692. Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
17P LOSS MUTATED	151	201	122
17P LOSS WILD-TYPE	69	197	133

Figure S692. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S693. Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
17P LOSS MUTATED	155	127	66	75	119	22	13
17P LOSS WILD-TYPE	109	42	77	150	84	29	7

Figure S693. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S694. Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
17P LOSS MUTATED	128	122	41	135	108	43
17P LOSS WILD-TYPE	161	41	49	155	75	17

Figure S694. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S695. Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
17P LOSS MUTATED	84	180	92	89	97	28
17P LOSS WILD-TYPE	55	90	116	127	85	18

Figure S695. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S696. Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
17P LOSS MUTATED	36	91	70	81	43	60	95	43	51
17P LOSS WILD-TYPE	30	32	114	105	31	53	64	30	32

Figure S696. Get High-res Image Gene #71: '17p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MRNA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S697. Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
17Q LOSS MUTATED	40	29	72
17Q LOSS WILD-TYPE	189	87	96

Figure S697. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'17q loss' versus 'MRNA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S698. Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
17Q LOSS MUTATED	21	76	44
17Q LOSS WILD-TYPE	138	190	44

Figure S698. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'17q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S699. Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
17Q LOSS MUTATED	68	39	26	139	0
17Q LOSS WILD-TYPE	262	93	269	155	29

Figure S699. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #3: 'CN_CNMF'

'17q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S700. Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
17Q LOSS MUTATED	31	37	33	67	8
17Q LOSS WILD-TYPE	187	146	112	72	80

Figure S700. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'17q loss' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S701. Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
17Q LOSS MUTATED	81	32	12	34	44	21	1
17Q LOSS WILD-TYPE	113	205	18	170	87	46	9

Figure S701. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'17q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S702. Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
17Q LOSS MUTATED	108	64	53
17Q LOSS WILD-TYPE	112	334	202

Figure S702. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'17q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S703. Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
17Q LOSS MUTATED	40	75	18	30	90	11	6
17Q LOSS WILD-TYPE	224	94	125	195	113	40	14

Figure S703. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'17q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S704. Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
17Q LOSS MUTATED	29	57	15	53	84	32
17Q LOSS WILD-TYPE	260	106	75	237	99	28

Figure S704. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S705. Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
17Q LOSS MUTATED	28	117	28	41	39	14
17Q LOSS WILD-TYPE	111	153	180	175	143	32

Figure S705. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'17q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S706. Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
17Q LOSS MUTATED	11	51	29	17	21	20	74	14	30
17Q LOSS WILD-TYPE	55	72	155	169	53	93	85	59	53

Figure S706. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'17q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S707. Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
17Q LOSS MUTATED	28	18	16	18	60	26
17Q LOSS WILD-TYPE	105	74	43	101	85	88

Figure S707. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'17q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0134 (Fisher's exact test), Q value = 0.018

Table S708. Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
17Q LOSS MUTATED	95	49	22
17Q LOSS WILD-TYPE	219	182	95

Figure S708. Get High-res Image Gene #72: '17q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'18p loss' versus 'MRNA_CNMF'

P value = 0.00207 (Fisher's exact test), Q value = 0.0033

Table S709. Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
18P LOSS MUTATED	57	32	69
18P LOSS WILD-TYPE	172	84	99

Figure S709. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0219 (Fisher's exact test), Q value = 0.028

Table S710. Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
18P LOSS MUTATED	38	96	24
18P LOSS WILD-TYPE	121	170	64

Figure S710. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S711. Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
18P LOSS MUTATED	121	46	42	106	5
18P LOSS WILD-TYPE	209	86	253	188	24

Figure S711. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #3: 'CN_CNMF'

'18p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S712. Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
18P LOSS MUTATED	50	87	37	42	13
18P LOSS WILD-TYPE	168	96	108	97	75

Figure S712. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18p loss' versus 'RPPA_CNMF'

P value = 0.00209 (Fisher's exact test), Q value = 0.0033

Table S713. Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
18P LOSS MUTATED	75	54	13	51	43	21	5
18P LOSS WILD-TYPE	119	183	17	153	88	46	5

Figure S713. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.034

Table S714. Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
18P LOSS MUTATED	78	122	62
18P LOSS WILD-TYPE	142	276	193

Figure S714. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S715. Gene #73: '18p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
18P LOSS MUTATED	84	91	26	38	55	16	10
18P LOSS WILD-TYPE	180	78	117	187	148	35	10

Figure S715. 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 = 2.3e-05

Table S716. Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
18P LOSS MUTATED	65	88	14	79	50	24
18P LOSS WILD-TYPE	224	75	76	211	133	36

Figure S716. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18p loss' versus 'MIRSEQ_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.02

Table S717. Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
18P LOSS MUTATED	50	95	50	51	55	16
18P LOSS WILD-TYPE	89	175	158	165	127	30

Figure S717. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'18p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S718. Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
18P LOSS MUTATED	21	58	36	46	20	39	39	25	33
18P LOSS WILD-TYPE	45	65	148	140	54	74	120	48	50

Figure S718. Get High-res Image Gene #73: '18p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'18q loss' versus 'MRNA_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.0016

Table S719. Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
18Q LOSS MUTATED	53	29	67
18Q LOSS WILD-TYPE	176	87	101

Figure S719. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'18q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0042 (Fisher's exact test), Q value = 0.0062

Table S720. Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
18Q LOSS MUTATED	32	93	24
18Q LOSS WILD-TYPE	127	173	64

Figure S720. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'18q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S721. Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
18Q LOSS MUTATED	119	48	41	108	5
18Q LOSS WILD-TYPE	211	84	254	186	24

Figure S721. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #3: 'CN_CNMF'

'18q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S722. Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
18Q LOSS MUTATED	54	86	34	48	13
18Q LOSS WILD-TYPE	164	97	111	91	75

Figure S722. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'18q loss' versus 'RPPA_CNMF'

P value = 0.00063 (Fisher's exact test), Q value = 0.0011

Table S723. Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
18Q LOSS MUTATED	73	56	14	48	43	24	6
18Q LOSS WILD-TYPE	121	181	16	156	88	43	4

Figure S723. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'18q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00341 (Fisher's exact test), Q value = 0.0051

Table S724. Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
18Q LOSS MUTATED	82	123	59
18Q LOSS WILD-TYPE	138	275	196

Figure S724. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'18q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S725. Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
18Q LOSS MUTATED	83	88	28	39	61	12	9
18Q LOSS WILD-TYPE	181	81	115	186	142	39	11

Figure S725. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'18q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S726. Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
18Q LOSS MUTATED	60	88	15	75	56	26
18Q LOSS WILD-TYPE	229	75	75	215	127	34

Figure S726. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'18q loss' versus 'MIRSEQ_CNMF'

P value = 0.00429 (Fisher's exact test), Q value = 0.0063

Table S727. Gene #74: '18q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
18Q LOSS MUTATED	44	104	49	52	53	14
18Q LOSS WILD-TYPE	95	166	159	164	129	32

Figure S727. 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 = 2.3e-05

Table S728. Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
18Q LOSS MUTATED	20	57	37	42	18	38	45	22	37
18Q LOSS WILD-TYPE	46	66	147	144	56	75	114	51	46

Figure S728. Get High-res Image Gene #74: '18q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MRNA_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 3e-04

Table S729. Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
19P LOSS MUTATED	39	10	47
19P LOSS WILD-TYPE	190	106	121

Figure S729. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S730. Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
19P LOSS MUTATED	101	13	6	76	1
19P LOSS WILD-TYPE	229	119	289	218	28

Figure S730. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #3: 'CN_CNMF'

'19p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S731. Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
19P LOSS MUTATED	28	49	17	40	2
19P LOSS WILD-TYPE	190	134	128	99	86

Figure S731. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19p loss' versus 'RPPA_CNMF'

P value = 0.00023 (Fisher's exact test), Q value = 0.00042

Table S732. Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
19P LOSS MUTATED	51	35	6	21	24	20	2
19P LOSS WILD-TYPE	143	202	24	183	107	47	8

Figure S732. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19p loss' versus 'RPPA_CHIERARCHICAL'

P value = 8e-05 (Fisher's exact test), Q value = 0.00016

Table S733. Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
19P LOSS MUTATED	55	78	26
19P LOSS WILD-TYPE	165	320	229

Figure S733. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S734. Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
19P LOSS MUTATED	71	50	7	15	49	3	1
19P LOSS WILD-TYPE	193	119	136	210	154	48	19

Figure S734. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S735. Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
19P LOSS MUTATED	55	58	3	24	44	12
19P LOSS WILD-TYPE	234	105	87	266	139	48

Figure S735. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S736. Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
19P LOSS MUTATED	43	80	23	12	25	9
19P LOSS WILD-TYPE	96	190	185	204	157	37

Figure S736. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S737. Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
19P LOSS MUTATED	21	29	5	27	11	19	38	16	26
19P LOSS WILD-TYPE	45	94	179	159	63	94	121	57	57

Figure S737. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S738. Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
19P LOSS MUTATED	40	11	3	10	44	12
19P LOSS WILD-TYPE	93	81	56	109	101	102

Figure S738. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'19p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S739. Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
19P LOSS MUTATED	83	31	6
19P LOSS WILD-TYPE	231	200	111

Figure S739. Get High-res Image Gene #75: '19p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'19q loss' versus 'MRNA_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 0.017

Table S740. Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
19Q LOSS MUTATED	33	9	34
19Q LOSS WILD-TYPE	196	107	134

Figure S740. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'19q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S741. Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
19Q LOSS MUTATED	88	11	6	58	1
19Q LOSS WILD-TYPE	242	121	289	236	28

Figure S741. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #3: 'CN_CNMF'

'19q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S742. Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
19Q LOSS MUTATED	26	41	17	30	2
19Q LOSS WILD-TYPE	192	142	128	109	86

Figure S742. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'19q loss' versus 'RPPA_CNMF'

P value = 0.00542 (Fisher's exact test), Q value = 0.0078

Table S743. Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
19Q LOSS MUTATED	42	30	4	20	16	17	1
19Q LOSS WILD-TYPE	152	207	26	184	115	50	9

Figure S743. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'19q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00231 (Fisher's exact test), Q value = 0.0036

Table S744. Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
19Q LOSS MUTATED	44	63	23
19Q LOSS WILD-TYPE	176	335	232

Figure S744. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'19q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S745. Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
19Q LOSS MUTATED	57	47	6	14	37	2	0
19Q LOSS WILD-TYPE	207	122	137	211	166	49	20

Figure S745. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'19q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S746. Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
19Q LOSS MUTATED	54	42	2	17	35	13
19Q LOSS WILD-TYPE	235	121	88	273	148	47

Figure S746. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S747. Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
19Q LOSS MUTATED	32	65	22	12	22	7
19Q LOSS WILD-TYPE	107	205	186	204	160	39

Figure S747. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'19q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S748. Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
19Q LOSS MUTATED	17	24	6	29	10	17	31	11	15
19Q LOSS WILD-TYPE	49	99	178	157	64	96	128	62	68

Figure S748. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'19q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.00025

Table S749. Gene #76: '19q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
19Q LOSS MUTATED	25	8	3	12	38	12
19Q LOSS WILD-TYPE	108	84	56	107	107	102

Figure S749. 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 = 4.5e-05

Table S750. Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
19Q LOSS MUTATED	69	25	4
19Q LOSS WILD-TYPE	245	206	113

Figure S750. Get High-res Image Gene #76: '19q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20p loss' versus 'MRNA_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.037

Table S751. Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
20P LOSS MUTATED	13	5	20
20P LOSS WILD-TYPE	216	111	148

Figure S751. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'20p loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00713 (Fisher's exact test), Q value = 0.01

Table S752. Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
20P LOSS MUTATED	8	16	14
20P LOSS WILD-TYPE	151	250	74

Figure S752. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20p loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S753. Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
20P LOSS MUTATED	30	5	7	49	2
20P LOSS WILD-TYPE	300	127	288	245	27

Figure S753. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #3: 'CN_CNMF'

'20p loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S754. Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
20P LOSS MUTATED	7	17	7	35	4
20P LOSS WILD-TYPE	211	166	138	104	84

Figure S754. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20p loss' versus 'RPPA_CNMF'

P value = 0.00042 (Fisher's exact test), Q value = 0.00075

Table S755. Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
20P LOSS MUTATED	32	11	2	11	15	8	0
20P LOSS WILD-TYPE	162	226	28	193	116	59	10

Figure S755. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20p loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S756. Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
20P LOSS MUTATED	36	28	15
20P LOSS WILD-TYPE	184	370	240

Figure S756. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20p loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S757. Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
20P LOSS MUTATED	26	13	4	6	43	0	1
20P LOSS WILD-TYPE	238	156	139	219	160	51	19

Figure S757. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20p loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S758. Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
20P LOSS MUTATED	18	22	2	6	41	4
20P LOSS WILD-TYPE	271	141	88	284	142	56

Figure S758. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S759. Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
20P LOSS MUTATED	9	47	11	10	7	3
20P LOSS WILD-TYPE	130	223	197	206	175	43

Figure S759. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20p loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S760. Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
20P LOSS MUTATED	6	8	4	7	3	12	37	3	7
20P LOSS WILD-TYPE	60	115	180	179	71	101	122	70	76

Figure S760. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20p loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00018

Table S761. Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
20P LOSS MUTATED	6	4	2	6	28	6
20P LOSS WILD-TYPE	127	88	57	113	117	108

Figure S761. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20p loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.0021

Table S762. Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
20P LOSS MUTATED	37	12	3
20P LOSS WILD-TYPE	277	219	114

Figure S762. Get High-res Image Gene #77: '20p loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'20q loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.00078 (Fisher's exact test), Q value = 0.0013

Table S763. Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
20Q LOSS MUTATED	3	9	11
20Q LOSS WILD-TYPE	156	257	77

Figure S763. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'20q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S764. Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
20Q LOSS MUTATED	13	5	4	33	2
20Q LOSS WILD-TYPE	317	127	291	261	27

Figure S764. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #3: 'CN_CNMF'

'20q loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S765. Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
20Q LOSS MUTATED	5	5	6	24	2
20Q LOSS WILD-TYPE	213	178	139	115	86

Figure S765. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'20q loss' versus 'RPPA_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.0011

Table S766. Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
20Q LOSS MUTATED	24	8	0	5	4	4	0
20Q LOSS WILD-TYPE	170	229	30	199	127	63	10

Figure S766. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'20q loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S767. Gene #78: '20q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
20Q LOSS MUTATED	25	16	4
20Q LOSS WILD-TYPE	195	382	251

Figure S767. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'20q loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S768. Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
20Q LOSS MUTATED	9	6	4	4	34	0	0
20Q LOSS WILD-TYPE	255	163	139	221	169	51	20

Figure S768. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'20q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S769. Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
20Q LOSS MUTATED	8	9	2	4	33	1
20Q LOSS WILD-TYPE	281	154	88	286	150	59

Figure S769. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S770. Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
20Q LOSS MUTATED	2	32	4	10	5	1
20Q LOSS WILD-TYPE	137	238	204	206	177	45

Figure S770. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'20q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S771. Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
20Q LOSS MUTATED	2	6	3	2	1	3	30	3	4
20Q LOSS WILD-TYPE	64	117	181	184	73	110	129	70	79

Figure S771. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'20q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S772. Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
20Q LOSS MUTATED	2	2	1	2	22	4
20Q LOSS WILD-TYPE	131	90	58	117	123	110

Figure S772. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'20q loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00234 (Fisher's exact test), Q value = 0.0037

Table S773. Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
20Q LOSS MUTATED	25	7	1
20Q LOSS WILD-TYPE	289	224	116

Figure S773. Get High-res Image Gene #78: '20q loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'21q loss' versus 'MRNA_CNMF'

P value = 0.039 (Fisher's exact test), Q value = 0.048

Table S774. Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
21Q LOSS MUTATED	34	13	37
21Q LOSS WILD-TYPE	195	103	131

Figure S774. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'21q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S775. Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
21Q LOSS MUTATED	86	18	12	55	8
21Q LOSS WILD-TYPE	244	114	283	239	21

Figure S775. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #3: 'CN_CNMF'

'21q loss' versus 'METHLYATION_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0012

Table S776. Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
21Q LOSS MUTATED	41	40	14	26	5
21Q LOSS WILD-TYPE	177	143	131	113	83

Figure S776. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'21q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00692 (Fisher's exact test), Q value = 0.0098

Table S777. Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
21Q LOSS MUTATED	49	40	6	41	33	9
21Q LOSS WILD-TYPE	240	123	84	249	150	51

Figure S777. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'21q loss' versus 'MIRSEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.031

Table S778. Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
21Q LOSS MUTATED	29	54	27	23	34	6
21Q LOSS WILD-TYPE	110	216	181	193	148	40

Figure S778. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'21q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.0021

Table S779. Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
21Q LOSS MUTATED	19	24	13	26	12	23	27	11	18
21Q LOSS WILD-TYPE	47	99	171	160	62	90	132	62	65

Figure S779. Get High-res Image Gene #79: '21q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MRNA_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 0.023

Table S780. Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
22Q LOSS MUTATED	120	52	64
22Q LOSS WILD-TYPE	109	64	104

Figure S780. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'22q loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S781. Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
22Q LOSS MUTATED	180	86	77	129	10
22Q LOSS WILD-TYPE	150	46	218	165	19

Figure S781. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #3: 'CN_CNMF'

'22q loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.00034

Table S782. Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
22Q LOSS MUTATED	73	200	120
22Q LOSS WILD-TYPE	147	198	135

Figure S782. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'22q loss' versus 'MRNASEQ_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.018

Table S783. Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
22Q LOSS MUTATED	143	69	61	104	77	19	8
22Q LOSS WILD-TYPE	121	100	82	121	126	32	12

Figure S783. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'22q loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 8.4e-05

Table S784. Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
22Q LOSS MUTATED	136	92	33	135	71	14
22Q LOSS WILD-TYPE	153	71	57	155	112	46

Figure S784. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.0056

Table S785. Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
22Q LOSS MUTATED	77	115	99	80	74	27
22Q LOSS WILD-TYPE	62	155	109	136	108	19

Figure S785. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'22q loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.026 (Fisher's exact test), Q value = 0.033

Table S786. Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
22Q LOSS MUTATED	34	53	71	79	43	61	60	31	40
22Q LOSS WILD-TYPE	32	70	113	107	31	52	99	42	43

Figure S786. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'22q loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.046

Table S787. Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
22Q LOSS MUTATED	73	41	28	57	58	40
22Q LOSS WILD-TYPE	60	51	31	62	87	74

Figure S787. Get High-res Image Gene #80: '22q loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MRNA_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.025

Table S788. Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
XP LOSS MUTATED	39	15	43
XP LOSS WILD-TYPE	190	101	125

Figure S788. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xp loss' versus 'MRNA_CHIERARCHICAL'

P value = 0.0195 (Fisher's exact test), Q value = 0.025

Table S789. Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	159	266	88
XP LOSS MUTATED	29	42	26
XP LOSS WILD-TYPE	130	224	62

Figure S789. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'xp loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S790. Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
XP LOSS MUTATED	81	21	6	81	3
XP LOSS WILD-TYPE	249	111	289	213	26

Figure S790. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #3: 'CN_CNMF'

'xp loss' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S791. Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
XP LOSS MUTATED	37	39	11	37	6
XP LOSS WILD-TYPE	181	144	134	102	82

Figure S791. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xp loss' versus 'RPPA_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.00035

Table S792. Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
XP LOSS MUTATED	56	37	10	24	21	11	2
XP LOSS WILD-TYPE	138	200	20	180	110	56	8

Figure S792. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xp loss' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S793. Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
XP LOSS MUTATED	61	72	28
XP LOSS WILD-TYPE	159	326	227

Figure S793. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xp loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S794. Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
XP LOSS MUTATED	66	35	11	20	53	5	0
XP LOSS WILD-TYPE	198	134	132	205	150	46	20

Figure S794. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xp loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S795. Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
XP LOSS MUTATED	59	36	3	32	51	9
XP LOSS WILD-TYPE	230	127	87	258	132	51

Figure S795. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S796. Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
XP LOSS MUTATED	28	70	38	15	29	6
XP LOSS WILD-TYPE	111	200	170	201	153	40

Figure S796. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xp loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0014

Table S797. Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
XP LOSS MUTATED	13	23	14	33	11	21	44	14	13
XP LOSS WILD-TYPE	53	100	170	153	63	92	115	59	70

Figure S797. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xp loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00137 (Fisher's exact test), Q value = 0.0022

Table S798. Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
XP LOSS MUTATED	30	10	6	14	39	15
XP LOSS WILD-TYPE	103	82	53	105	106	99

Figure S798. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xp loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00101 (Fisher's exact test), Q value = 0.0017

Table S799. Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
XP LOSS MUTATED	72	29	13
XP LOSS WILD-TYPE	242	202	104

Figure S799. Get High-res Image Gene #81: 'xp loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'xq loss' versus 'MRNA_CNMF'

P value = 0.0338 (Fisher's exact test), Q value = 0.042

Table S800. Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	229	116	168
XQ LOSS MUTATED	41	13	39
XQ LOSS WILD-TYPE	188	103	129

Figure S800. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #1: 'MRNA_CNMF'

'xq loss' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S801. Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	330	132	295	294	29
XQ LOSS MUTATED	83	21	7	74	4
XQ LOSS WILD-TYPE	247	111	288	220	25

Figure S801. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #3: 'CN_CNMF'

'xq loss' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S802. Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	218	183	145	139	88
XQ LOSS MUTATED	37	47	10	32	7
XQ LOSS WILD-TYPE	181	136	135	107	81

Figure S802. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'xq loss' versus 'RPPA_CNMF'

P value = 0.00421 (Fisher's exact test), Q value = 0.0062

Table S803. Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	194	237	30	204	131	67	10
XQ LOSS MUTATED	50	40	10	24	20	12	1
XQ LOSS WILD-TYPE	144	197	20	180	111	55	9

Figure S803. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #5: 'RPPA_CNMF'

'xq loss' versus 'RPPA_CHIERARCHICAL'

P value = 0.00056 (Fisher's exact test), Q value = 0.00098

Table S804. Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	220	398	255
XQ LOSS MUTATED	52	77	28
XQ LOSS WILD-TYPE	168	321	227

Figure S804. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'xq loss' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 2.3e-05

Table S805. Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	264	169	143	225	203	51	20
XQ LOSS MUTATED	67	37	13	23	42	6	0
XQ LOSS WILD-TYPE	197	132	130	202	161	45	20

Figure S805. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'xq loss' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 4.5e-05

Table S806. Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	289	163	90	290	183	60
XQ LOSS MUTATED	58	44	4	35	40	7
XQ LOSS WILD-TYPE	231	119	86	255	143	53

Figure S806. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 6.4e-05

Table S807. Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	139	270	208	216	182	46
XQ LOSS MUTATED	29	60	39	14	35	9
XQ LOSS WILD-TYPE	110	210	169	202	147	37

Figure S807. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'xq loss' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00241 (Fisher's exact test), Q value = 0.0038

Table S808. Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7	CLUS_8	CLUS_9
ALL	66	123	184	186	74	113	159	73	83
XQ LOSS MUTATED	15	25	13	34	11	24	35	16	13
XQ LOSS WILD-TYPE	51	98	171	152	63	89	124	57	70

Figure S808. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'xq loss' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.014

Table S809. Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	133	92	59	119	145	114
XQ LOSS MUTATED	32	12	5	17	34	14
XQ LOSS WILD-TYPE	101	80	54	102	111	100

Figure S809. Get High-res Image Gene #82: 'xq loss' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'xq loss' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00283 (Fisher's exact test), Q value = 0.0044

Table S810. Gene #82: 'xq loss' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	314	231	117
XQ LOSS MUTATED	71	29	14
XQ LOSS WILD-TYPE	243	202	103

Figure S810. 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/BRCA-TP/22531238/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BRCA-TP/22595637/BRCA-TP.transferedmergedcluster.txt
Number of patients = 1080
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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